You may do this:
ffmpeg -i input.mkv -c:v copy -c:a libfaac out.mp4
Or if there is no joy, try fixing the internal bitstream
Conversion to stereo and asc:
ffmpeg -i input.mkv -c:v copy -c:a libfaac \
-bsf:a aac_adtstoasc -ac 2 -ar 48000 -ab 256k \
out.mkv
If it is 5.1, surround and the voices are hard to hear it is because the dialog is on the center channel and you are only hearing the off-mike from the R & L channels but the music and sound effects are booming.
You can compensate for this with dolby-II filter to get the surround channel cut way down and the center channel split into stereo, and combine them all into right and left stereo channels.
ffmpeg -i input.mkv -c:v copy -c:a libfaac -bsf:a aac_adtstoasc \
-af aresample=matrix_encoding=dplii -ac 2 -ar 48000 -ab 256k \
out.mkv
Can you help us please and give us the exact command you're using and the complete, uncut output that FFmpeg produces? Which operating system are you on? And lastly: Do you have to use FFmpeg? Please [edit] your question. – slhck – 2012-10-02T18:48:12.520