ffmpeg comes with a tool to re-order the MP4 “atoms” (Seriously don’t ask what are MP4 atoms it’s geek for the sake of geek).

find the file in ffmpeg_src/tools/qt-faststart.c

compile with gcc


gcc qt-faststart.c -o qt-faststart


And run.


/path/to/qt-faststart /path/to/src_vid.mp4 /path/to/output.mp4


NOTE: This only seems to work for h264 encoded videos (libx264).