Hi, and welcome to LQ!
I don't believe it would be a 'wrong version'. And FWIW, I'm using Ubuntu on an ex-Win98 machine with no problems at all. The only possibility I can think of right now is that maybe your Windows partition is encrypted. Not sure if MS even updated 2000 to do that, but try this and see what happens:
Boot the Live CD/DVD. Open a terminal and type:
This will ignore the current partition and repartition the entire disk as /dev/hda.
Then run the installer again.
Hope this helps.