I've been having issues with videos I downloaded from youtube. When I try to play the video with VLC, sometimes it won't play or it quits in the middle of the video. This happens on some of the videos (not all). Then I found this tool FLV MetaData Injector from http://www.buraks.com/flvmdi/ and it seems like it fixes this issue!
There are two files that you need to download from the site above. The links are right in the middle of the page.
Try and see if it works for you as well.
cheers.