root@localhost:/media/c562c662-acad-4cd2-9a3a-e5b30fc367e9/downloads# ffmpeg -i input.mkv -acodec copy -vcodec copy output.mp4FFmpeg version SVN-r0.5.6-4:0.5.6-3, Copyright (c) 2000-2009 Fabrice Bellard, et al.
  configuration: --extra-version=4:0.5.6-3 --prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-vdpau --enable-bzlib --enable-libdirac --enable-libgsm --enable-libopenjpeg --enable-libschroedinger --enable-libspeex --enable-libtheora --enable-libvorbis --enable-pthreads --enable-zlib --disable-stripping --disable-vhook --enable-runtime-cpudetect --enable-gpl --enable-postproc --enable-swscale --enable-x11grab --enable-libfaad --enable-libdc1394 --enable-shared --disable-static
  libavutil     49.15. 0 / 49.15. 0
  libavcodec    52.20. 1 / 52.20. 1
  libavformat   52.31. 0 / 52.31. 0
  libavdevice   52. 1. 0 / 52. 1. 0
  libavfilter    0. 4. 0 /  0. 4. 0
  libswscale     0. 7. 1 /  0. 7. 1
  libpostproc   51. 2. 0 / 51. 2. 0
  built on Dec 31 2011 16:14:46, gcc: 4.4.5

Seems stream 0 codec frame rate differs from container frame rate: 47.95 (48000/1001) -> 24.00 (24/1)
Input #0, matroska, from 'input.mkv':
  Duration: 00:55:43.54, start: 0.000000, bitrate: N/A
    Stream #0.0(eng): Video: h264, yuv420p, 1280x720, PAR 1:1 DAR 16:9, 24 tbr, 1k tbn, 47.95 tbc
    Stream #0.1(eng): Audio: ac3, 48000 Hz, 5.1, s16
Output #0, mp4, to 'output.mp4':
    Stream #0.0(eng): Video: 0x0000, yuv420p, 1280x720 [PAR 1:1 DAR 16:9], q=2-31, 90k tbn, 1k tbc
    Stream #0.1(eng): Audio: ac3, 48000 Hz, 5.1, s16
Stream mapping:
  Stream #0.0 -> #0.0
  Stream #0.1 -> #0.1
[mp4 @ 0x1a91b90]track 1: codec frame size is not set
Could not write header for output file #0 (incorrect codec parameters ?)
root@localhost:/media/c562c662-acad-4cd2-9a3a-e5b30fc367e9/downloads#