[Damn... I see there was another reply in the meantime!]
Pete,
The CMOS battery only maintains the real time clock when the computer is powered off. The typical symptom of a flat battery is the computer losing the date and time when you power it down. A flat battery won't make your clock run slow (or fast) while the computer is up and running.
As to what is making your clock run fast, that's a bit of a mystery to me. Are you or your computer moving at relativistic speeds?
Could be rogue time synchronization software if you're running any (third party or the Windows Time Service). Have you ever seen it happen before?
I use Dimension4 to keep my Windows clock accurate and it seems to work well:
http://www.thinkman.com/dimension4/default.htm
Cheers,
Rick.