Does 2000 have a service for that? I honestly can't remember. Try disabling it and see if it lets you make the change. You said the time is right, but will it let you change it? How old is the cmos battery?
That CMOS battery is hell of old, I could look it up...
My records show I bought the mobo (MSI KT3 Ultra2) in Sept. 2002. So, the battery's likely that old.
Edit: I downloaded the Atomic.exe available at the link that bruceb posted, ran it and I couldn't detect that anything happened at all. No installation, no indication of anything.
I had just RUN net stop w32time (in the command window), the command window disappeared. No indication of anything in particular having happened. When checking out my Atomic.exe download I noticed something else in my downloads directory, having been downloaded Sept. 15, 2015, being NetTimeSetup-314.exe. So, I just ran that and in installing it first indicated that it was "uninstalling" so I infer that it was already running (i.e. I probably installed it last September), which might have something to do with the problem in general! The program was configured to run at the end of installation (as long as I left the checkbox checked) and I let it run. It's running in the background continuously, is I believe that's how it's set up on my machine. I guess it insures that the computer's clock is accurate. It's correct now, however the machine still thinks I'm in Arizona!
Really, it won't be a problem until the next time DLST changes, but that will happen, presumably in November, I guess. It would be nice to get the machine to realize what the new DST rules are and just take care of itself in regards to that. And of course it would be cool if it would realize I'm on PDT.