Odds are that Windows 2000 bootup entry is just a phantom, because while technically possible, it's rather difficult to get two operating systems onto the same partition. Even more so when we're talking two copies of Windows.
So just look for some program that can edit the boot menu, or boot.ini file -- I wouldn't recommend doing it by hand unless you know what you're doing -- and you can remove that.
I have two operating systems (Windows 2000 and Windows XP) installed on the same partition. How do I delete one of them? I have Partition Magic installed, if anyone has instructions using that program.