The iTunes update has had a numerous amount of bugs since it's release(iTunes 7). My library got jacked up the first time through(had a backup though, like everyone should), and now that I got it working, if I do any kind of 'multitasking', such as...opening IE or Firefox, or browsing My Documents, the music skips. Seems to be a major performance issue since the update. I downloaded an update patch or whatever couple weeks ago, and it was a little better. It stopped screwing up my library for one. I actually had to do some reading on the updates and changes to make sure it wasn't 'user error' and me being dumb. Looking around online though seems to be a common problem.
iTunes works flawlessly on my Mac though.