I'm having a heck of time trying to get WINFF to work with FFMPEG....I've followed all suggestions with the new preset file, etc. 
Here's what I get when attempting to convert an mp4 to avi:
ffmpeg version 0.10.4-6:0.10.4-0ubuntu0jon2 Copyright (c) 2000-2012 the FFmpeg developers
  built on Jun 12 2012 23:02:05 with gcc 4.6.3
  configuration: --extra-version='6:0.10.4-0ubuntu0jon2' --arch=amd64 --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu --disable-stripping --enable-vaapi --enable-vdpau --enable-bzlib --enable-gnutls --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --enable-runtime-cpudetect --enable-libfreetype --enable-libpulse --enable-vaapi --enable-librtmp --enable-gpl --enable-postproc --enable-x11grab --enable-libcdio --enable-version3 --enable-libdc1394 --shlibdir=/usr/lib/x86_64-linux-gnu --enable-shared --disable-static
  avutil      configuration: --extra-version='6:0.10.4.0ubuntu0jon2.2' --arch=amd64 --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu --disable-stripping --enable-vaapi --enable-vdpau --enable-bzlib --enable-gnutls --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --enable-runtime-cpudetect --enable-libfreetype --enable-libpulse --enable-vaapi --enable-libopenjpeg --enable-libmp3lame --enable-librtmp --enable-frei0r --enable-libopencv --enable-gpl --enable-postproc --enable-x11grab --enable-libcdio --enable-libx264 --enable-version3 --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libdc1394 --shlibdir=/usr/lib/x86_64-linux-gnu --enable-shared --disable-static
  swscale     configuration: --extra-version='6:0.10.4.0ubuntu0jon2.2' --arch=amd64 --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu --disable-stripping --enable-vaapi --enable-vdpau --enable-bzlib --enable-gnutls --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --enable-runtime-cpudetect --enable-libfreetype --enable-libpulse --enable-vaapi --enable-libopenjpeg --enable-libmp3lame --enable-librtmp --enable-frei0r --enable-libopencv --enable-gpl --enable-postproc --enable-x11grab --enable-libcdio --enable-libx264 --enable-version3 --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libdc1394 --shlibdir=/usr/lib/x86_64-linux-gnu --enable-shared --disable-static
  swresample  configuration: --extra-version='6:0.10.4.0ubuntu0jon2.2' --arch=amd64 --prefix=/usr --libdir=/usr/lib/x86_64-linux-gnu --disable-stripping --enable-vaapi --enable-vdpau --enable-bzlib --enable-gnutls --enable-libgsm --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --enable-libvpx --enable-runtime-cpudetect --enable-libfreetype --enable-libpulse --enable-vaapi --enable-libopenjpeg --enable-libmp3lame --enable-librtmp --enable-frei0r --enable-libopencv --enable-gpl --enable-postproc --enable-x11grab --enable-libcdio --enable-libx264 --enable-version3 --enable-libopencore-amrnb --enable-libopencore-amrwb --enable-libvo-aacenc --enable-libvo-amrwbenc --enable-libdc1394 --shlibdir=/usr/lib/x86_64-linux-gnu --enable-shared --disable-static
  libavutil      51. 35.100 / 51. 35.100
  libavcodec     53. 61.100 / 53. 61.100
  libavformat    53. 32.100 / 53. 32.100
  libavdevice    53.  4.100 / 53.  4.100
  libavfilter     2. 61.100 /  2. 61.100
  libswscale      2.  1.100 /  2.  1.100
  libswresample   0.  6.100 /  0.  6.100
  libpostproc    52.  0.100 / 52.  0.100
Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/home/pablo/Desktop/Complete/am.mp4':
  Metadata:
    major_brand     : isom
    minor_version   : 1
    compatible_brands: isom
    creation_time   : 2011-09-08 11:43:25
  Duration: 00:21:28.95, start: 0.000000, bitrate: 1214 kb/s
    Stream #0:0(und): Video: h264 (High) (avc1 / 0x31637661), yuv420p, 720x404 [SAR 32219:32400 DAR 319:180], 1083 kb/s, 23.98 fps, 23.98 tbr, 24k tbn, 47.95 tbc
    Metadata:
      creation_time   : 2011-09-08 11:43:25
      handler_name    : 
    Stream #0:1(und): Audio: aac (mp4a / 0x6134706D), 48000 Hz, stereo, s16, 125 kb/s
    Metadata:
      creation_time   : 2011-09-08 11:43:25
      handler_name    : 
Please use -b:a or -b:v, -b is ambiguous
Unknown encoder 'libxvid'
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