Thanks you both!
@DVDdoug: I prefere a bash script with no GUI because of no needing of a desktop environment
I've noticed that the converted video has the front/back issue just using the libfaac codec. The original audio is in two different formats, dca and ac3. I've tried converting thus the original audio directly in aac or MP3, but it seems to have a bad distortion (like a metallic sound... weird)...
ffmpeg -i MyVideo.mkv
FFmpeg version 0.5.1, Copyright (c) 2000-2009 Fabrice Bellard, et al.
configuration: --prefix=/opt/local --disable-vhook --enable-gpl --enable-postproc --enable-swscale --enable-avfilter --enable-avfilter-lavf --enable-libmp3lame --enable-libvorbis --enable-libtheora --enable-libdirac --enable-libschroedinger --enable-libfaac --enable-libfaad --enable-libxvid --enable-libx264 --enable-nonfree --mandir=/opt/local/share/man --enable-shared --enable-pthreads --cc=/usr/bin/gcc-4.2 --arch=x86_64
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 1. 4. 0 / 1. 4. 0
libswscale 1. 7. 1 / 1. 7. 1
libpostproc 51. 2. 0 / 51. 2. 0
built on May 17 2010 19:18:13, gcc: 4.2.1 (Apple Inc. build 5659)
Seems stream 0 codec frame rate differs from container frame rate: 47.95 (48000/1001) -> 23.98 (24000/1001)
Input #0, matroska, from 'MyVideo.mkv':
Duration: 02:41:41.72, start: 0.000000, bitrate: N/A
Stream #0.0(ita): Video: h264, yuv420p, 1920x1080, PAR 1:1 DAR 16:9, 23.98 tbr, 1k tbn, 47.95 tbc
Stream #0.1(ita): Audio: dca, 48000 Hz, 5.1, s16
Stream #0.2(ita): Subtitle: 0x0000
Stream #0.3(ita): Subtitle: 0x0000
Stream #0.4(ita): Audio: ac3, 48000 Hz, 5.1, s16
At least one output file must be specified
I don't know what dca is, but on VLC the AC3 track works great...