This may not solve your problem, but you should feed the video files into a diagnostic utility like the ones listed here http://www.moviecodec.com/topics/61931p1.html to check their integrity. Some viruses will deliberately destroy certain file types (I think one of the early worms used to destroy mp3 files).
If it recognizes the files as AVI with the xvid codec, then I’m not sure what to suggest.
BTW what error message(s) are you getting? If it’s an access denied, it may simply be because of the reformat. You would need to take ownership of the files again to be able to access them. http://support.microsoft.com/kb/308421
