First off check the ide connection with the motherboard.
You should go to device manager and look for it (my computer (right click properties) -> hardware -> device manager -> dvd cdrom -> see if it is there.
Why would you do this: I am running 3 hard drives but using 2. One of them is not ntfs, it is linux, so windows cant use it, but I can see it frome device manager. So it will see all of your drives even if windows can't use them for some add reason.
one issue might be some bad ide controls or something.