Yeah, I've been having this problem for an unacceptably long amount of time. It's not a Vista problem, as I've had this problem on both XP and Vista since at least 2006 (when I first got my iPod). It's also not an iPod specific problem, as it happened with my 2nd gen Nano, and also my new Classic 80GB. It is EXTREMELY frustrating. What's worse is, the files are still ON my iPod. I can disconnect, and play them just fine through the iPod, just not on iTunes.
http://forums.ilounge.com/archive/index.php/t-210242.html
rickhuizinga at that link has a logical sounding reason of why it happens, but that doesn't explain why this hasn't been fixed yet.