ok then, best way (although marginally not the easiest) is to put linux in as the primary master drive and then basically lie to windows to trick it into thinking that it is on the master channel after all when you tell it to boot it. I'd assume that you currently boot to linux via lilo? bluey / purpley screen allowing you to choose a few differnt versions of linux to boot to? if so, boot up and as root edit /etc/lilo.conf and to the end add:
map-drive = 0x80 # Logically swap the drives so that when they
to = 0x81 # are accessed via the BIOS, the second drive
map-drive = 0x81 # will appear as the first and the first as
to = 0x80
and then run "lilo" as root. reboot and then that option should be available to you, and with the windows drive being connected as pri slave, should boot fine. the fundamental benefit of this little diversion means that you *never* *ever* touch the windows drive at all with anything linux related, so you have a full dual boot system you can remove simply by replacing win2k on the master channel, no risk whatsoever.