Same problem.

Here's output from ffmpeg:

FFmpeg version 0.5-svn17737+3:0.svn20090303-1ubuntu6, Copyright (c) 2000-2009 
Fabrice Bellard, et al.
  configuration: --enable-gpl --enable-postproc --enable-swscale 
--enable-x11grab --extra-version=svn17737+3:0.svn20090303-1ubuntu6 
--prefix=/usr --enable-avfilter --enable-avfilter-lavf --enable-libgsm 
--enable-libschroedinger --enable-libspeex --enable-libtheora 
--enable-libvorbis --enable-pthreads --disable-stripping --disable-vhook 
--enable-libdc1394 --disable-armv5te --disable-armv6 --disable-armv6t2 
--disable-armvfp --disable-neon --disable-altivec --disable-vis --enable-shared 
--disable-static
  libavutil     49.15. 0 / 49.15. 0
  libavcodec    52.20. 0 / 52.20. 0
  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 Apr 10 2009 23:18:41, gcc: 4.3.3

Seems stream 0 codec frame rate differs from container frame rate: 50.00
(50/1) -> 25.00 (25/1)

Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'input.mp4':
  Duration: 01:50:03.93, start: 0.000000, bitrate: 1809 kb/s
    Stream #0.0(und): Video: h264, yuv420p, 704x288, 25 tbr, 25 tbn, 50 tbc
    Stream #0.1(und): Audio: ac3, 48000 Hz, stereo, s16

Output #0, avi, to 'output.avi':
    Stream #0.0(und): Video: libx264, yuv420p, 704x288, q=2-31, 90k tbn, 25 tbc
    Stream #0.1(und): Audio: mp2, 48000 Hz, stereo, s16, 64 kb/s

Stream mapping:
  Stream #0.0 -> #0.0
  Stream #0.1 -> #0.1

-- 
mplayer cannot find audiocodec 0x332D6361 while ffmeg can
https://bugs.launchpad.net/bugs/416941
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