I want to join two mp4 files to create a single one. The video streams are encoded in h264 and the audio in aac. I can not re-encode the videos to another format due to computational reasons. Also, I cannot use any gui programs, all processing must be performed with linux command line utilities. FFmpeg cannot do this for mpeg4 files so instead I used MP4Box

e.g. MP4Box -add video1.mp4 -cat video2.mp4 newvideo.mp4

unfortunately the audio gets all mixed up. I thought that the problem was that the audio was in aac so I transcoded it in mp3 and used again MP4Box. In this case the audio is fine for the first half of newvideo.mp4 (corresponding to video1.mp4) but then their is no audio and I cannot navigate in the video also. My next thought was that the audio and video streams had some small discrepancies in their lengths that I should fix. So for each input video I splitted the video and audio streams and then joined them with the -shortest option in ffmpeg.

thus for the first video I ran

 avconv -y -i video1.mp4 -c copy -map 0:0 videostream1.mp4

 avconv -y -i video1.mp4 -c copy -map 0:1 audiostream1.m4a

 avconv -y -i videostream1.mp4 -i audiostream1.m4a  -c copy -shortest  video1_aligned.mp4

similarly for the second video and then used MP4Box as previously. Unfortunately this didn't work either. The only success I had was when I joined the video streams separetely (i.e. videostream1.mp4 and videostream2.mp4) and the audio streams (i.e. audiostream1.m4a and audiostream2.m4a) and then joined the video and audio in a final file. However, the synchronization is lost for the second half of the video. Concretelly, there is a 1 sec delay of audio and video. Any suggestions are really welcome.