Shouldn't be affecting things, I've had Diskeeper running in the background for years with no ill effects.
To be of any more help, we really need to know what you're trying to play and your computers specs.
Playing HD (720p plus) stuff on an underpowered computer could easily cause this sort of issue, as could playing 'normal' videos on anything about a P3 or lower.
Cheers
-Leezer-