I too am having this issue. Have hundreds of movies.
When I play a movie stored on my ext'l HDD via VLC, Quicktime, WD HDTV's or other video programs on computers, no issues with the files at all. When using files in my iTunes library on my computer, play without an issue.
When I try to watch movies on AppleTV, 3rd Gen, some movies have audio sync issues, off by several seconds; these delays do not exist during any other useage scenarios mentioned above, only with apple TV. Some MP4 files will not even open, just sit their loading and loading for minutes. Sometimes they start, other times, not. 😕Main issue is when a movie starts, then after only a couple minutes, the screen blacks out, and audio continues.
I back out to the menu, then attempt to resume, and in many cases, the file will begin at either where it left off. The screen is always blacked out. Have not been able to back out, resume, and watch for another few minutes like others.
Have fast forwarded then pushed play, to test the bug and to see what would happen. Sometimes I hear audio at a later stage in the movie (with blacked out screen); most times it will begin playing at the exact same place at some random spot in the movie. With one file, when I back out again, push start from beginning, the film will start half way through a movie at the exact same place each time. (This has happened only with one film thus far). Very odd.
Have deleted a file, thinking it was corrupted, then used a back up file of the original to attempt to reformat, and correct any errors in metadata. Nothing working.
In that I have new 2012 MBP Retina, mid-2010 Imac 2.8 i5, Ipad 3, Ipad touches, and now two iPhone 5's, would like everything to just work.
Any help is appreciated. Thanks in advance