More information:
AMD64 3700+
2 gigs of RAM
Creative X-Fi Sound
Nvidia 7900GT
Apps that are generally open and might be having their files scanned:
Trillian
iTunes
Firefox 2.0
Thunderbird 1.5
uTorrent
Ultramon
Last.FM
iSproggler
SyncBackSE
This has happened with every version I've tried on Vista, going all the way back to October, so it's not just a recent thing. It's a "dropout" kinda skip, where it sounds like the music has stopped for a second and then restarted. It doesn't happen with any regularity that I've noticed, just sorta randomly. It seems to happen maybe a few times an hour at random points.