Trouble with Video Format *

I am attempting to upload a bunch of videos for a script process. I am using Final Cut Pro and the new version will not allow me to export the audio and video independently. So almost every export option like apple pro res, Uncompressed 8bit/10bit etc, Psychopy is either not able to read or creates a compressed version of that video file and it create a cracking noise during the audio of these videos. What other formats would work with psychopy that would help me eliminate this problem?
I would have to change all of my files from MOV to the one format that actually works which is H.264, but that would be a hassle. Is there a reason Psychopy is not able to successfully read and run these MOV files or the other versions that Final Cut Pro gives me besides H.264?