Certain video files don't work with XMBC

I have a central Multimedia PC that I record all my favorite TV shows on using Windows Media Center. When I try to access these files from ATV using XBMC certain video files will not play. They are all recorded using the same Windows Media Center so am unsure why only certain files would play while others will not. Could this have to do with the video quality selected (ie. Best, Better, Good, Fair)?