What you mean by running your files through the player? Streaming to it? Connecting an external hard drive over USB and using it as a media player?
Again, I doubt that the player has a problem with MPEG-2 (no matter how you are playing the file), but perhaps the file itself is problematic. In which case, you might have to recompress it. I'm loathe to suggest HandBrake, but if you just want to watch it, you might give it a try.