I had this problem trying to dual boot Win98 and XP. I finally found somewhere that XP has to be installed after any other versions of Windows for this to work, no matter what kind of partitions you are using. Once I reinstalled XP after 98 was installed, it then started giving me a prompt at boot up to choose which one to boot into. It is something to do with the Master Boot Record. This is probably true with a XP/2000 dual boot setup.