I've split your post into a new thread. Responding via an almost 7 year old thread is not helping.
Check marks are set in the video database using the files tables.
You haven't mentioned any of the actions leading up to this situation, but it's possible that the files table of the video database got corrupted somehow.
Once that happens, the only two options are to either restore a previous backup (*cough*), or simply rescrape your files in to a new video database.
Perhaps you can provide a
debug log (wiki) for starters so we can see with what type of hardware we're dealing with.