I think it might be WMP
This all sounds a bit familiar to me. My WMP (XP Pro SP2) decided to start playing silly buggers a few weeks ago after an update from Microdaft. certain files it will not play properly and etc.etc.
The way I get around this now is just use another media player. There are loads maybe already on your machine from Media software like Roxio, or maybe Quicktime, or whatever. Failing that, download a freebie like MusicMatch, RealPlayer or similar, even if it is just used to narrow the problem down.
I now use Winamp as my default player and it seems to work fine now.
Good luck! :-)