I havent paid much attention to this but thinking back has happened to quite a few of my videos and games.
I have tried using the videos and games on a CRT and LCD monitor with same results, and have reinstalled Vista many times since then.
I was playing my Sonic CD on an emulator and noticed that the game doesnt run that smooth, I have dropped it to as low as 640 by 480 with no difference, made so no plugins or filters were used etc it runs fast but not smooth.
I use VLC for my video playback and notice often again the frame rate seems fine(maybe) but its not moving smoothly.
I only realised how laggy both were after using a regular dvd player for a change on a tv I use sometimes as a CRT monitor(though have a real CRT as well) and noticed the picture quality was better and the movie ran fast and smooth.
3 gigs DDR2 ram OCZ
600W OCZ Stealhstream psu