I meant to post yesterday. I tried iTunes (9.0.3.15) via USB from my laptop, and it sounded OK on several tracks. This was with WinXP on an Asus 1000H netbook. I assume you're not just talking about something which I'd need golden ears to detect.
One possibility is that there's something on your machine which is grabbing the processor from time to time. I have had that kind of problem before, though some players and servers seem much more resistant to it than others.
Hope you're making progress.