Spanner... suggested checking the hardware jumpers on the back of both drives, to make sure the C is set to MASTER and D is set to SLAVE properly - that SHOULD fix the problem. (the master and slave jumper settings are usually marked in really small letters).
If that didn't work, try disconnecting the D drive (both power and signal cables) and reinstall Windows (hopefully you don't have a lot on the new C drive yet). After all is well, try re-connecting the D drive and see if that works.
If that fails, put in the OLD C drive (the one you took out) and back up the important data on floppies
before exploring other options. Good luck!