We need to know what version of AE and PPro down to the last decimal point, the codec used for the movies you are having problems with because .mov is only a container that can hold hundreds of codec variants, and the OS version down to the last decimal.
Off hand I'd guess that you have some mp4 files that are not completely compatible with AE due to your setup or preferences or you have installed some 3rd party video codec, video player, or other video app that is mucking up the works.
Mac Version 10.9.2
AE Version: 10.5.0.253
PPro Version: 5.5.2 (003 (MC:258762)
VLC is the only program I have that has 3rd party codecs. We got it with a peice of hardware. Do you think I should install/reinstall the drivers of that hardware? What would you like to know about my setup/preferences in AE?
EDIT: How can I fiond the codec of a quicktime video? Google hasn't helped me.
Codec is AAC, H.264, 2 Channel Audio, etc.
Opening up a file with VLC gives me 516 streams ( ! ) with
Stream 0 having Audio | MPEG AAC Audio (mp4a) | Stereo | 48000 Hz
Stream(s) 1 - 516 having Video | H264 - MPEG-4 AVC (part 10)(avc1) | 1920x1080 | Frame rate of 23.9744...
Some, however, have the (correct) decoding of Planer 4:2:0 YUV, as of which I believe this causes the Purp/Green colors & sometimes dropped frame.
Edit: (More Info)
Due note that the movies where recorded as AVCHD, then opened into Quicktime and then saved as a .MOV for greater flexibility with different programs.
Would it be worth it to try and find the .MTS files again, and use those?
Or, if they have gone missing, what would I do anyways?
Try loading your file in the Adobe Media Encoder and export them to QuickTime Jpeg at High quality. If the export is good you have a frame based production master to work on.
Mp4 files are usually not suitable in any form for production. If transcoding to a DI in AME does not work then re-record using something other than AVCHD (lousy lossy intraframe amateur mess most of the time)