I have a pc here that I think has a defective controller on the motherboard.
The problem started when the cd rom appeared not to work, when I looked closer the secondary IDE contoller was showing a yellow exclamation mark in device properties. I tried to reload the drivers without success so I eventually decided to reload windows 98SE. I moved the cd rom to be slave to the hard drive.
Once reloaded the secondary channel was installed so I naturally thought I had cracked it but when I reconnected the cd-rom to the second IDE the old problem reared its head. I have changed the cable just incase that was the problem.
I can only conclude that the second IDE is faulty. My thoughts at the moment are to install a PCI IDE controller card, I cannot put the cd as slave cos there is a second hard drive.
Has anyone any other ideas other than fitting the PCI card?

You could try hooking some other device to the supposedly bad IDE channel to rule out a bad CD-ROM or a jumper setting.