This sounds like a hardware configuration problem to me.
Check the jumper settings on your drives and make sure you have one master and one slave per channel. The C drive should be the master
for IDE channel #1 and drive D the master for IDE Channel #2. You can have one master and one slave connected to one IDE port never two masters or two slaves. Since you did not have the drives partitioned you should end up with your original configuration of two separate hard disks under the version of Windows you are using. You probably have both drives set up as master. plug the drives separately into the IDE ports 1&2 of your motherboard and set them as masters for each. set up your CD-Rom and other drives as slaves and connect them to the secondary channels(doesn't matter which one)and check your drive booting order in your system BIOS.
Good Luck!