camaro -
Sounds like you are seeing the option of booting to Windows 2000 twice at boot from the boot loader?
If this is the case, first make sure that both choices will actually boot to W2K by selecting each choice on two different boots.
If that is the case, all you need to do is edit your boot.ini file - c:\boot.ini with notepad. You'll see the last two lines that look something like this (mine is modified so use just as reference

)
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Micro sucks Winblows XP Home Edition" /fastdetect /KERNEL=LOGOOS.EXE
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Micro sucks Winblows XP Home Edition" /fastdetect /KERNEL=LOGOOS.EXE
All you need to do is wipe the duplicate line out and save. Reboot and that should be it.
BTW, getting rid of an errant Linux install is the fdisk /mbr from a 98 boot disk.
Hope that helps!
Mike