Our mind-reading abilities are limited, but I'm guessing these are MPEG-4 videos (such as H.264, .mkv, .divx, .mp4, .m4v)?
You are probably seeing the result of too aggressive compression that s not done properly to the specification. You are posting in an AE forum, do you get the same result in AE?
MPEG-4 is correct
I would normally agree with an side-effect of some nature from improper procedure, but the exposed content is very different.
Haven't tried AE yet, but I'm willing to try something. Any suggestions? I thought this forum might have more individuals experienced with this sort of thing.
What Jonas said. This kind of thing happens with footage that has too long intervals between I-frames, either because the compression scheme is out of spec or the files are damaged. That can especially be a problem with decoders/ players that do not read far ahead for performance reasons and may not be able to reconstruct the frames fully. If it looks okay in AE or Premiere Pro, there should not be much to worry. also running such files through ffmpeg/ MPEG Streamclip/ Handbrake or similar tools with a quick trtanscode can help to establish proper formatting of the MPEG stream and it will behave much better.
If you are willing to try anything, how about importing the file into AE?
I'm guessing the encoding is corrupt or non-standard since you are seeing the same problem in several programs.
How to get the correct frames? Well, if you are seeing different frames each time you play through it, you may have to do a manual save of each frame and then try to put them in the correct order.
I'd try to open the file in several other video programs and see if it works in any of them. Have you tried Handbrake, for example?