Here is the command I am using to combine multiple videos:
ffmpeg -i 75_540_38HQ2.mp4 -i 76_70_20.mp4 -i 76_173_80.mp4 -i 81_186_35.mp4 -vcodec copy -acodec copy M
MP4Box does work without breaking the audio. I did the following to obtain good results:
Download the latest Linux deb build from the gpac web site: http://gpac.wp.mines-telecom.fr/downloads/gpac-nightly-builds/
Use the -force-cat option
Sample command line:
MP4Box -force-cat -add in1.mp4 -cat in2.mp4 -cat in3.mp4 ... out.mp4
Some minor comments:
The above way is important, as the latest version of MP4Box distributed with Linux Mint 13 is buggy, and does result in corrupted audio.
-force-cat is important, as the video format tag was changed from AVC to avc3 without it.