itunes library - some movies "playback not supported"

So I have several hundred movies that I've ripped from my DVDs into digital format on an external harddrive. They're all organized and whatnot into folders by genre etc and so on, as I'm sure many folks have....

The issue that I have is that while all were working previously, some are now throwing up the dreaded "Video playback is not supported" message when I try to play them in iTunes. The thumbnail in the library is now just the generic grey music notes, and I cannot copy it onto any other devices (or more importantly, play it on my apple TV). The files themselves are fine: I can play them on my computer to my heart's content. Even deleting them from the library and relinking them does not work.

I would say this is impacting roughly 15-20% of my video files...and it's incredibly frustrating as the only way to get them back is to delete the original video file, re-rip from dvd, and re import...which would be great if I hadn't ditched a majority of my DVDs.

I have already tried installing iTunes for older video cards, reinstalling quick time etc as those were the sommon solutions.

Any suggestions for how to fix this?