I have the same bug on an amd64 machine with onboard sound.

I also tried "dpkg-reconfigure vlc vlc-nox vlc-data" as well as installing the pulse plugin without any inprovements.

When vlc is started from terminal with

vlc --verbose 2

I get the following: (there is a lot more output over this part)

[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 375052087
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 375535914
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 375860898
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 376343090
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 376674480
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 376919744
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 377225626
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 377528555
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 377747809
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 377998994
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 378258871
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 378691025
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 379061199
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 379425643
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 379797712
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 380334970
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 380674304
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 380961782
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 381249306
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 381496070
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 381666929
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 381908089
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 382124473
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 382303001
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 382500693
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 382704625
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 382919282
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 383151015
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 383336134
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 383854720
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 384390961
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 384546785
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 384724332
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 384949350
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 385188177
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 385370565
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 385510867
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 385640633
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 385789858
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 385870684
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 385979835
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 386039491
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 386116679
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 386221648
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 386354183
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 386487474
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 386581006
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 386718689
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 386885308
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 387058067
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 387233030
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 387405420
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 387545822
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 387945964
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 388446309
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 388591994
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 389139418
[0x1393ec8] mkv demux debug: |   |   + Seek
 m_el[mi_level] == NULL
 arrrrrrrrrrrrrg Up cannot escape itself
[0x1393ec8] mkv demux debug: |   - unknown seekhead reference at 389290468
[0x1393ec8] mkv demux debug: |   |   + Seek
[0x1393ec8] mkv demux debug: |   |   + Unknown (N7libebml8EbmlVoidE)
[0x1393ec8] mkv demux debug: |   - cues at 389354026
[0x1393ec8] mkv demux debug: |   + Cues
[0x1393ec8] mkv demux debug: |   - loading cues done.
[0x1393ec8] mkv demux debug: |   + Preload Unknown (N7libebml8EbmlVoidE)
[0x1393ec8] mkv demux debug: |   + Information
[0x1393ec8] mkv demux debug: |   + Tracks
[0x1393ec8] mkv demux debug: |   + Preload Unknown (N7libebml8EbmlVoidE)
[0x1393ec8] mkv demux debug: |   + Cluster
[0x1393ec8] mkv demux debug: found 7 es
[0x1424598] main input debug: selecting program id=0
[0x1393ec8] mkv demux debug: original frame size vobsubs: 720x576
[0x1393ec8] mkv demux debug: original frame size vobsubs: 720x576
[0x1393ec8] mkv demux debug: original frame size vobsubs: 720x576
[0x1393ec8] mkv demux debug: original frame size vobsubs: 720x576
[0x1393ec8] mkv demux debug: original frame size vobsubs: 720x576
[0x1393ec8] mkv demux debug: Starting the UI Hook
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0xff7e48] main generic debug: thread started
[0xff7e48] main generic debug: thread (mkv event thread handler) created at priority 0 (demux.cpp:199)
[0x1393ec8] main demux debug: using demux module "mkv"
[0x1393ec8] main demux debug: TIMER module_need() : 550,668 ms - Total 550,668 ms / 1 intvls (Avg 550,668 ms)
[0xd370e8] qt4 interface debug: Updating the geometry
[0x1424598] main input debug: looking for a subtitle file in /home/jkr/Videos/Angel.s01-05.Complete.dvdrip.x264/Angel.s01.1999.dvdrip.x264/
[0x14188b8] main decoder debug: looking for decoder module: 31 candidates
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0x14188b8] avcodec decoder debug: libavcodec initialized (interface 0x341400)
[0x14188b8] avcodec decoder debug: ffmpeg codec (H264 - MPEG-4 AVC (part 10)) started
[0x14188b8] main decoder debug: using decoder module "avcodec"
[0x14188b8] main decoder debug: TIMER module_need() : 22,412 ms - Total 22,412 ms / 1 intvls (Avg 22,412 ms)
[0x14188b8] main decoder debug: thread started
[0x14188b8] main decoder debug: thread (decoder) created at priority 0 (input/decoder.c:315)
[0x20318f8] main decoder debug: looking for decoder module: 31 candidates
[0x20318f8] main decoder debug: using decoder module "faad"
[0x20318f8] main decoder debug: TIMER module_need() : 0,838 ms - Total 0,838 ms / 1 intvls (Avg 0,838 ms)
[0x20318f8] main decoder debug: thread started
[0x20318f8] main decoder debug: thread (decoder) created at priority 5 (input/decoder.c:315)
[0x2077fe8] main decoder debug: looking for decoder module: 31 candidates
[0x2077fe8] avcodec decoder debug: libavcodec already initialized
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0x2077fe8] main decoder debug: using decoder module "spudec"
[0x2077fe8] main decoder debug: TIMER module_need() : 5,828 ms - Total 5,828 ms / 1 intvls (Avg 5,828 ms)
[0x2077fe8] main decoder debug: thread started
[0x2077fe8] main decoder debug: thread (decoder) created at priority 0 (input/decoder.c:315)
[0x2077fe8] spudec decoder debug: invalid starting packet (size < 4 or pts <=0)
[0x2077fe8] spudec decoder debug: spu size: 0, i_pts: 0 i_buffer: 128
[0x1424598] main input debug: idx1=-1(en) idx2=-1(da)
[0x1424598] main input debug: idx1=-1(fi) idx2=-1(da)
[0x1424598] main input debug: idx1=-1(no) idx2=-1(da)
[0x1424598] main input debug: idx1=-1(sv) idx2=-1(da)
[0x1424598] main input debug: `/home/jkr/Videos/Angel.s01-05.Complete.dvdrip.x264/Angel.s01.1999.dvdrip.x264/Angel.1x01.City_Of.x264.mkv' successfully opened
[0x1424598] main input error: Invalid PCR value in ES_OUT_SET_(GROUP_)PCR !
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0x1424598] main input error: Invalid PCR value in ES_OUT_SET_(GROUP_)PCR !
[0x1424598] main input debug: Buffering 0%
[0xd370e8] qt4 interface debug: New caching: 0
[0xd370e8] qt4 interface debug: New caching: 0
[0x20318f8] faad decoder warning: decoded zero sample
[0x20318f8] faad decoder debug: AAC SBR (channels: 2, samplerate: 48000)
[0x1424598] main input debug: creating aout
[0x7f6540107958] main audio output debug: looking for audio output module: 4 candidates
[0x1424598] main input debug: Stream buffering done (339 ms in 11 ms)
[0xd370e8] qt4 interface debug: New caching: 100
[0xd370e8] qt4 interface debug: New caching: 100
[0x7f6540107958] alsa audio output debug: opening ALSA device `default'
[0x7f6540107958] main audio output debug: thread (aout) created at priority 15 (alsa.c:687)
[0x7f6540107958] main audio output debug: using audio output module "alsa"
[0x7f6540107958] main audio output debug: TIMER module_need() : 162,091 ms - Total 162,091 ms / 1 intvls (Avg 162,091 ms)
[0x7f6540107958] main audio output debug: thread started
[0x7f6540107958] main audio output debug: output 'fl32' 48000 Hz Stereo frame=1 samples/8 bytes
[0x7f6540107958] main audio output debug: mixer 'fl32' 48000 Hz Stereo frame=1 samples/8 bytes
[0x7f6540107958] main audio output debug: no need for any filter
[0x7f6540107958] main audio output debug: looking for audio mixer module: 3 candidates
[0x7f6540107958] main audio output debug: using audio mixer module "float32_mixer"
[0x7f6540107958] main audio output debug: TIMER module_need() : 0,896 ms - Total 0,896 ms / 1 intvls (Avg 0,896 ms)
[0x7f6540107958] main audio output debug: input 'fl32' 48000 Hz Stereo frame=1 samples/8 bytes
[0x2133398] main audio filter debug: looking for audio filter module: 1 candidate
[0x2133398] scaletempo audio filter debug: format: 48000 rate, 2 nch, 4 bps, fl32
[0x2133398] scaletempo audio filter debug: params: 30 stride, 0,200 overlap, 14 search
[0x2133398] scaletempo audio filter debug: 1,000 scale, 1440,000 stride_in, 1440 stride_out, 1152 standing, 288 overlap, 672 search, 2400 queue, fl32 mode
[0x2133398] main audio filter debug: using audio filter module "scaletempo"
[0x2133398] main audio filter debug: TIMER module_need() : 2,534 ms - Total 2,534 ms / 1 intvls (Avg 2,534 ms)
[0x7f6540107958] main audio output debug: filter(s) 'fl32'->'fl32' 52800 Hz->48000 Hz Stereo->Stereo
[0x2130c28] main audio output debug: looking for audio filter module: 24 candidates
[0x2130c28] main audio output debug: using audio filter module "bandlimited_resampler"
[0x2130c28] main audio output debug: TIMER module_need() : 6,164 ms - Total 6,164 ms / 1 intvls (Avg 6,164 ms)
[0x7f6540107958] main audio output debug: found a filter for the whole conversion
[0x20318f8] main decoder debug: End of audio preroll
[0x1424598] main input debug: Decoder buffering done in 171 ms
[0x1424598] main input debug: no usable vout present, spawning one
[0x2361f58] main spu text debug: looking for text renderer module: 2 candidates
[0x2371218] main generic debug: thread (fontlist builder) created at priority 0 (freetype.c:473)
[0x2361f58] freetype spu text debug: using fontsize: 2
[0x2361f58] main spu text debug: using text renderer module "freetype"
[0x2361f58] main spu text debug: TIMER module_need() : 3,444 ms - Total 3,444 ms / 1 intvls (Avg 3,444 ms)
[0x2371218] main generic debug: thread started
[0x2363a88] main scale debug: looking for video filter2 module: 20 candidates
[0x7f6540107958] main audio output warning: PTS is out of range (12991), dropping buffer
[0x7f6540107958] main audio output warning: PTS is out of range (-28527), dropping buffer
[0x7f6540107958] main audio output warning: buffer is 43335 in advance, triggering downsampling
[0x2371218] freetype generic debug: Building font database...
[0x2371218] freetype generic debug: Finished building font database.
[0x2371218] freetype generic debug: Took 1425 microseconds
[0x2371218] main generic debug: thread ended
[0x2363a88] swscale scale debug: 32x32 chroma: YUVA -> 16x16 chroma: YUVA with scaling using Bicubic (good quality)
[0x2363a88] main scale debug: using video filter2 module "swscale"
[0x2363a88] main scale debug: TIMER module_need() : 16,526 ms - Total 16,526 ms / 1 intvls (Avg 16,526 ms)
[0x2364b58] main scale debug: looking for video filter2 module: 20 candidates
[0x2364b58] yuvp scale debug: YUVP to YUVA converter
[0x2364b58] main scale debug: using video filter2 module "yuvp"
[0x2364b58] main scale debug: TIMER module_need() : 5,993 ms - Total 5,993 ms / 1 intvls (Avg 5,993 ms)
[0x235d018] main video output debug: window size: 785x576
[0x235d018] main video output debug: looking for video output module: 6 candidates
[0x235d018] xvideo video output debug: adaptor 0, port 82, format 0x32315659 (YV12) planar
[0x216fc38] main window debug: looking for xwindow module: 3 candidates
[0x216fc38] qt4 window debug: requesting video...
[0xd370e8] qt4 interface debug: Video was requested -1, -1
[0xd370e8] qt4 interface debug: Video is resizing to: 785 576
[0xd370e8] qt4 interface debug: Updating the geometry
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
QPainter::begin: Paint device returned engine == 0, type: 1
QPainter::begin: Paint device returned engine == 0, type: 1
[0x216fc38] main window debug: using xwindow module "qt4"
[0x216fc38] main window debug: TIMER module_need() : 100,442 ms - Total 100,442 ms / 1 intvls (Avg 100,442 ms)
[0x235d018] xvideo video output debug: XShm video extension v1.1 (without pixmaps, opcode: 140)
[0x235d018] xvideo video output debug: Window manager supports NetWM
[0x235d018] xvideo video output debug: Window manager supports _NET_WM_STATE_FULLSCREEN
[0x235d018] xvideo video output debug: Window manager supports _NET_WM_STATE_ABOVE
[0x235d018] xvideo video output debug: Window manager supports _NET_WM_STATE_BELOW
[0x235d018] main video output debug: using video output module "xvideo"
[0x235d018] main video output debug: TIMER module_need() : 115,102 ms - Total 115,102 ms / 1 intvls (Avg 115,102 ms)
[0x235d018] main video output debug: Deinterlacing available
[0x235d018] main video output debug: got 16 direct buffer(s)
[0x235d018] main video output debug: pic render sz 720x576, of (0,0), vsz 720x576, 4cc I420, ar 785:576, sar 157:144, msk r0x0 g0x0 b0x0
[0x235d018] main video output debug: pic in sz 720x576, of (0,0), vsz 720x576, 4cc I420, ar 785:576, sar 157:144, msk r0x0 g0x0 b0x0
[0x235d018] main video output debug: pic out sz 720x576, of (0,0), vsz 720x576, 4cc I420, ar 785:576, sar 157:144, msk r0x0 g0x0 b0x0
[0x235d018] main video output debug: direct render, mapping render pictures 0-14 to system pictures 1-15
[0x235d018] qt4 video output debug: Qt: Entering Fullscreen
[0x2171e48] main filter debug: looking for video filter2 module: 1 candidate
[0x2171e48] main filter debug: using video filter2 module "adjust"
[0x2171e48] main filter debug: TIMER module_need() : 2,785 ms - Total 2,785 ms / 1 intvls (Avg 2,785 ms)
[0x235d018] main video output debug: Filter 'adjust' (0x2171e48) appended to chain
[0x14188b8] main decoder debug: End of video preroll
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (389141), playing silence
[0x235d018] main video output debug: Post-processing available
[0x235d018] main video output debug: Filter 'adjust' (0x2171e48) removed from chain
[0x2171e48] main filter debug: removing module "adjust"
[0x2171e48] main filter debug: looking for video filter2 module: 1 candidate
[0x2171e48] main filter debug: using video filter2 module "adjust"
[0x2171e48] main filter debug: TIMER module_need() : 0,588 ms - Total 0,588 ms / 1 intvls (Avg 0,588 ms)
[0x235d018] main video output debug: Filter 'adjust' (0x2171e48) appended to chain
[0x235d018] main video output warning: late picture skipped (463395 > -2532)
[0x235d018] main video output warning: late picture skipped (427134 > -2532)
[0x235d018] main video output warning: late picture skipped (391197 > -2532)
[0x235d018] main video output warning: late picture skipped (354956 > -2532)
[0x2361f58] freetype spu text debug: using fontsize: 36
[0x2196808] main blend debug: looking for video blending module: 1 candidate
[0x2196808] blend blend debug: chroma: YUVA -> I420
[0x2196808] main blend debug: using video blending module "blend"
[0x2196808] main blend debug: TIMER module_need() : 0,438 ms - Total 0,438 ms / 1 intvls (Avg 0,438 ms)
[0x235d018] main video output warning: late picture skipped (66480 > -4332)
[0x235d018] main video output warning: late picture skipped (36754 > -4332)
[0x235d018] main video output warning: late picture skipped (6701 > -4332)
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (354351), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (430344), playing silence
[0x235d018] main video output warning: late picture skipped (305248 > -6879)
[0x235d018] main video output warning: late picture skipped (425248 > -6879)
[0x235d018] main video output warning: late picture skipped (385248 > -6879)
[0x235d018] main video output warning: late picture skipped (345248 > -6879)
[0x235d018] main video output warning: late picture skipped (275668 > -6879)
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (311425), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (399081), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (405149), playing silence
[0x7f6540107958] alsa audio output error: cannot write: Broken pipe
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (22530), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (432735), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (408334), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (413339), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (432858), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (407402), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (276353), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (450512), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (435002), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (389609), playing silence
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (298163), playing silence
[0x7f6540107958] alsa audio output error: cannot write: Broken pipe
[0xd36888] main libvlc debug: deactivating the playlist
[0xe36078] main playlist debug: Deactivate
[0xe36078] main playlist debug: incoming request - stopping current input
[0xe36078] main playlist debug: dying input
[0x1424598] main input debug: control type=0
[0x1424598] main input debug: control: stopping input
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x235d018] main video output warning: late picture skipped (20610 > -7476)
[0x7f6540107958] main audio output warning: output date isn't PTS date, requesting resampling (44961)
[0x7f6540107958] alsa audio output debug: recovered from buffer underrun
[0x7f6540107958] main audio output debug: audio output is starving (513404), playing silence
[0xe36078] main playlist debug: dying input
[0x14188b8] main decoder warning: can't get output picture
[0x14188b8] avcodec decoder debug: ffmpeg codec (H264 - MPEG-4 AVC (part 10)) stopped
[0x14188b8] main decoder debug: removing module "avcodec"
[0x14188b8] main decoder debug: killing decoder fourcc `avc1', 0 PES in FIFO
[0x235d018] main video output debug: [0] 4 0
[0x235d018] main video output debug: [1] 4 0
[0x235d018] main video output debug: [2] 4 0
[0x235d018] main video output debug: [3] 4 0
[0x235d018] main video output debug: [4] 4 0
[0x235d018] main video output debug: [5] 2 0
[0x235d018] main video output debug: [6] 2 0
[0x235d018] main video output debug: [7] 4 0
[0x235d018] main video output debug: [8] 2 0
[0x235d018] main video output debug: [9] 4 0
[0x235d018] main video output debug: [10] 4 0
[0x235d018] main video output debug: [11] 2 0
[0x235d018] main video output debug: [12] 4 0
[0x235d018] main video output debug: [13] 4 0
[0x235d018] main video output debug: [14] 4 0
[0x1424598] main input debug: saving a free vout
[0x20318f8] main decoder debug: removing module "faad"
[0x20318f8] main decoder debug: killing decoder fourcc `mp4a', 0 PES in FIFO
[0x2133398] main audio filter debug: removing module "scaletempo"
[0x2130c28] main audio output debug: removing module "bandlimited_resampler"
[0x7f6540107958] main audio output debug: thread ended
[0x7f6540107958] main audio output debug: removing module "alsa"
[0x7f6540107958] main audio output debug: removing module "float32_mixer"
[0x1424598] main input debug: releasing aout
[0x2077fe8] main decoder debug: removing module "spudec"
[0x2077fe8] main decoder debug: killing decoder fourcc `spu ', 0 PES in FIFO
[0xff7e48] main generic debug: thread ended
[0x1393ec8] mkv demux debug: Stopping the UI Hook
[0x1393ec8] main demux debug: removing module "mkv"
[0x10f49d8] main stream debug: removing module "stream_filter_record"
[0x14028b8] main access debug: removing module "access_file"
[0x1424598] main input debug: Program doesn't contain anymore ES
[0xe36078] main playlist debug: dead input
[0x1424598] main input debug: thread ended
[0x235d018] main video output debug: destroying useless vout
[0xd370e8] qt4 interface debug: IM: Deleting the input
[0xd370e8] qt4 interface debug: Updating the geometry
[0xd370e8] qt4 interface debug: Updating the geometry
[0x235d018] qt4 video output debug: Qt: Entering Fullscreen
[0x1424598] main input debug: TIMER input launching for 'Angel.1x01.City_Of.x264.mkv' : 622,814 ms - Total 622,814 ms / 1 intvls (Avg 622,814 ms)
[0x235d018] main video output debug: Filter 'adjust' (0x2171e48) removed from chain
[0x2171e48] main filter debug: removing module "adjust"
[0x216fc38] qt4 window debug: releasing video...
[0xd370e8] qt4 interface debug: Video is not needed anymore
[0xd370e8] qt4 interface debug: Updating the geometry
[0x216fc38] main window debug: removing module "qt4"
[0x235d018] main video output debug: removing module "xvideo"
[0x2196808] main blend debug: removing module "blend"
[0x2361f58] main spu text debug: removing module "freetype"
[0x2364b58] main scale debug: removing module "yuvp"
[0x2363a88] main scale debug: removing module "swscale"
[0xe36078] main playlist debug: saving Media Library to file /home/jkr/.local/share/vlc/ml.xspf
[0xe36078] main playlist debug: looking for playlist export module: 1 candidate
[0xe36078] main playlist debug: using playlist export module "export"
[0xe36078] main playlist debug: TIMER module_need() : 0,606 ms - Total 0,606 ms / 1 intvls (Avg 0,606 ms)
[0xe36078] main playlist debug: removing module "export"
[0xe36078] main playlist debug: Deactivated
[0xd36888] main libvlc debug: removing all services discovery tasks
[0xd36888] main libvlc debug: removing all interfaces
[0xd370e8] qt4 interface debug: Quitting the Qt4 Interface
[0xd370e8] qt4 interface debug: destroying the main Qt4 interface
[0xd370e8] qt4 interface debug: Destroying the main interface
[0xd370e8] main interface debug: removing module "qt4"
[0xd36ad8] main interface debug: removing module "signals"
[0xe3e998] main interface debug: removing module "screensaver"
[0xe47bb8] main interface debug: removing module "inhibit"
[0xe437d8] main interface debug: removing module "hotkeys"
[0xd36888] main libvlc debug: removing playlist
[0xe36078] main playlist debug: Destroyed
[0xd36888] main libvlc debug: TIMER ML Load : Total 5,898 ms / 1 intvls (Avg 5,898 ms)
[0xd36888] main libvlc debug: TIMER Items array build : Total 0,299 ms / 2 intvls (Avg 0,149 ms)
[0xd36888] main libvlc debug: TIMER ML Dump : Total 0,924 ms / 1 intvls (Avg 0,924 ms)
[0xd36888] main libvlc debug: removing stats
[0xd36888] main libvlc debug: removing module "memcpymmxext"
[0xd36888] main libvlc debug: writing plugins cache /home/jkr/.cache/vlc/plugins-04081e.dat
Interface initialization failed


It seems to me that the ' Invalid PCR value in ES_OUT_SET_(GROUP_)PCR ! ' sounds important ?