In order to successfully dual-boot Win9x and NT4/2K with NT's boot loader, both drives need to be connected when *both* OSes are installed. You just cannot add a drive with the OS already installed and expect things to work. 11 out of 10 times, I guarantee that it will NOT work.
Provided that C: in your Win2K side is FAT/FAT32, you'll need to reinstall Win9x with both drives attached (use "setup /ntldr" from DOS).
-SUO