Okay, I removed the IDE controller from Windows, then replaced the old IDE cable that came with the system with a new one. I successfully booted with both drives connected. For the moment it would seem as if it's working.
I'm still a little concerned as when I first turn the computer on the HD accesses for a few seconds. Normally it only comes on for a split second. I hope that's nothing to be concerned about, but some part of me is afraid it might be.
You still haven't mentioned how your drives are set up/ cabled...
Sorry, I didn't think it was important. Usually I plug the master into the end of the cable, and the slave in the middle. Although I did try swapping that arrangement. Which didn't seem to matter either way. My old IDE cable (for the CDROM drives) was a 40 wire cable that came with the system when I bought it. The new one I just installed is an 80 wire cable. The HD cable is a newer 80 wire cable that came with the HD when I bought it.