Look for a hidden system file in the root of the C: drive called BOOT.INI. Change the file attributes to turn off hidden and read only. Open the file in notepad and you should see two lines that start with "multi(..." and one that says c:\="Windows 98".
You need to delete the line starting with "multi" that points to the old install. If you have your W2K set as default then look on the 'default=' line and it will tell you which of the following lines is the good one. If both lines are exactly alike (because you installed in the same location as the privious install) then pick the second line and delete it.
Make sure to make a backup copy of the boot.ini before doing this and reset the file attributes back to their original state whenyou are done.
Hope this helps...