HI I know this is an old thread, but I’ve found one work around- -if you have motion and the files are playable in quicktime player (X) then you can create a motion project of the same size, duration, frame rate etc., and export it via motion
be sure frame blending is NOT checked, and export directly from motion (don’t send to compressor since it might hang)
this is a re-encode, as opposed to a transcode, so it’s not ideal, but it’s pretty high quality and certainly beats simply exporting from quicktime player as a compressed mp4.