difference between MP4 and MP4v2

[anctop]

I'd like to ask a question about the difference between mp4 and mp4v2.

I have some .flv (H264 video, AAC audio) files retrieved using RTMPDump from a video streaming site.
When I tried to re-mux them into .mp4 with Avidemux ("copy" for video/audio output and "MP4 Muxer" for output format), the process died prematurely and a dialogue box said "Too short, The video has been saved but seems to be incomplete." and a subsequent one said "Failed, File xxxx was NOT saved correctly." The resultant .mp4 was broken.
However, when I repeated the procedure but changed the format to "MP4v2 Muxer", then the process could finish without complaint. The resultant .mp4 seemed to be intact.

It may be concluded that MP4v2 is preferable for my task, but I want to ask :
is that MP4v2 just more fault tolerant, or that there is some workaround to fix the error in the source .flv without impairing the integrity ?

[mean]

it's just different low level libraries
mp4v2 is more tolerant but could also more easily cause sync issue because of that

[anctop]

it's just different low level libraries
mp4v2 is more tolerant but could also more easily cause sync issue because of that

Thank you for the info.
The resultant .mp4 files play as fine as the original .flv files.
May I assume that there is no sync issue in my case ? How can I check them ?

[mean]

If it plays in sync with VLC, it's fine