Comment 6 for bug 942166

Just to help you dig further:

On a different computer and from a very fresh *L*ubuntu oneiric desktop installation, I ran the very same thing, with the very same (sad) results...

$ transcode -J stabilize -i input_mjpeg.avi
transcode v1.1.5 (C) 2001-2003 Thomas Oestreich, 2003-2009 Transcode Team
libdvdread: Encrypted DVD support unavailable.
************************************************
** **
** No css library available. See **
** /usr/share/doc/libdvdread4/README.Debian **
** for more information. **
** **
************************************************
libdvdnav:DVDOpenFileUDF:UDFFindFile /VIDEO_TS/VIDEO_TS.IFO failed
libdvdnav:DVDOpenFileUDF:UDFFindFile /VIDEO_TS/VIDEO_TS.BUP failed
libdvdread: Can't open file VIDEO_TS.IFO.
libdvdread: Encrypted DVD support unavailable.
************************************************
** **
** No css library available. See **
** /usr/share/doc/libdvdread4/README.Debian **
** for more information. **
** **
************************************************
libdvdnav:DVDOpenFileUDF:UDFFindFile /VIDEO_TS/VIDEO_TS.IFO failed
libdvdnav:DVDOpenFileUDF:UDFFindFile /VIDEO_TS/VIDEO_TS.BUP failed
libdvdread: Can't open file VIDEO_TS.IFO.
[transcode] V: auto-probing | input_mjpeg.avi (OK)
[transcode] V: import format | MJPEG in RIFF data, AVI (module=ffmpeg)
[transcode] A: auto-probing | input_mjpeg.avi (OK)
[transcode] A: import format | PCM in RIFF data, AVI (module=raw)
[transcode] V: AV demux/sync | (1) sync AV at initial MPEG sequence
[transcode] V: import frame | 1280x720 1.78:1 encoded @ 16:9
[transcode] V: bits/pixel | 0.130 (low)
[transcode] V: decoding fps,frc | 15.000,13
[transcode] V: video format | YUV420 (4:2:0) aka I420
[transcode] A: import format | 0x1 PCM [8000, 8,1] 64 kbps
[transcode] A: export | disabled
[transcode] V: encoding fps,frc | 15.000,13
[transcode] A: bytes per frame | 533 (533.333333)
[transcode] A: adjustment | 336@1000
[transcode] V: IA32/AMD64 accel | sse3 sse2 sse mmx cmove asm
[transcode] warning: no option -o found, encoded frames send to "/dev/null"
[transcode] warning: no option -y found, option -o ignored, writing to "/dev/null"
[transcode] V: video buffer | 10 @ 1280x720 [0x2]
[transcode] A: audio buffer | 10 @ 8000x1x8
[import_raw.so] v0.3.3 (2008-11-23) (video) RGB/YUV | (audio) PCM
[import_ffmpeg.so] v0.1.15 (2008-01-28) (video) ffmpeg: MS MPEG4v1-3/MPEG4/MJPEG
[filter_stabilize.so] v0.93 (2011-11-09) extracts relative transformations of
    subsequent frames (used for stabilization together with the
    transform filter in a second pass)
[filter_stabilize.so] Fieldsize: 96, Maximal translation: 90 pixel
[filter_stabilize.so] Number of used measurement fields: 13 out of 40
[filter_stabilize.so] Image Stabilization Settings:
[filter_stabilize.so] shakiness = 5
[filter_stabilize.so] accuracy = 5
[filter_stabilize.so] stepsize = 6
[filter_stabilize.so] algo = 1
[filter_stabilize.so] mincontrast = 0.250000
[filter_stabilize.so] show = 0
[filter_stabilize.so] result = input_mjpeg.avi.trf
[export_null.so] v0.1.2 (2001-08-17) (video) null | (audio) null
[import_raw.so] tcextract -x pcm -i "input_mjpeg.avi" -d 0 | tcextract -a 0 -x pcm -d 0 -t raw
transcode: symbol lookup error: /usr/lib/transcode/import_ffmpeg.so: undefined symbol: avcodec_init

But there, one can see there's *no* Medibuntu package implied !

$ dpkg --list libavcodec*
un libavcodec-extra-53 <none>
ii libavcodec53 4:0.7.3-0ubuntu0.11.10.1 Libav codec library

Repeating the same research :

# locate libavcodec.so
/usr/lib/libavcodec.so.53 (symlink to below)
/usr/lib/libavcodec.so.53.6.0
/usr/lib/i686/cmov/libavcodec.so.53 (symlink to below)
/usr/lib/i686/cmov/libavcodec.so.53.6.0

# readelf -Ws /usr/lib/libavcodec.so.53.6.0|grep avcodec_init
  1395: 003ca330 31 FUNC GLOBAL DEFAULT 12 avcodec_init@@LIBAVCODEC_53
# readelf -Ws /usr/lib/i686/cmov/libavcodec.so.53.6.0|grep avcodec_init
  1395: 003ca7b0 31 FUNC GLOBAL DEFAULT 12 avcodec_init@@LIBAVCODEC_53

Well, is there anything more I could do to help?
I'm sure my poor coding skills won't help, but I will test any package you may patch.