A while back, I ran Win2K under VMWare 2.0 on Linux and had problems as I was trying to keep a real multi-boot configuration (with Win2K pre-installed on a separate partition).
Good point. I never could get that sort of thing to work.
First off, it doesn't like to be booted back and forth, as its hardware keeps changing, which confuses the bejeezus out of Windows.
Secondly, even after I gave up trying to boot it natively, it still never quite worked right from its own partition. It just worked a hell of a lot better from a virtual disk. And the redo-able disk (or whatever it's called) that they have is really cool. It'll keep your Windows install from ever getting corrupted.
I don't ever remember having clock issues, but, then I wasn't paying a lot of attention. I can't imagine why NTP wouldn't work right.