first, you may have to take the sides off your computer so you can see the physical hard drives and motherboard and other objects. Make sure that BOTH harddrives have the POWER and IDE cables connected, and the CD ROM has its IDE and POWER cables connected...

the power cable is a small plastic plug USUALLY with Black Red and Yellow wires behind it. The IDE cables are usually gray. ENSURE that both hard drives share the same IDE cable and the CD rom is on its separate one.

Second idea, which may also solve the problem, when you load up your computer, go into BIOS. Im not sure how familiar you are with BIOS, but one of the options allows your computer to automatically set the settings for your HardDrives and Cd Roms... Usually there is a option that sets your BIOS to load the best settings, or load the default settings, usually with a F?? Key... (F11 or F10 usually)...

A third possibility that you should check when the computer is taken apart is your jumper settings. If you have two Masters or two Slaves, it ill cause many conflicts. These should be located in the back of the hard drive. Make sure your main hard drive is set to Master and your backup, is, obviously slave. A small plastic piece should fix these settings if they are incorrect.

Also, a friend of my father had this problem before, and found simply that his computer was incapable of hosting multiple hard drives. I'm not sure exactly the date when multiple harddrives were implemented.

But it definately sounds like you have the secondary hard drive and the CDROM on the same IDE cable and on the same setting if only one shows.