I had this problem a few weeks back - both were fully listed in Device Manager in Safe Mode but not in normal use.
Eventually I worked out that attempts to improve the air flow through my case by moving the cables etc had caused the IDE cable from the two drives to be pulled out of the main IDE cable plug socket on the motherboard.
I had naturally inspected that the drives' plugs and power supplies were correctly plugged in but the other end was hidden by the realigned cabling.
Reinsterted the secondary cable plug into socket and voila!
I am currently runninng windows 98 on my drive, and i recently found out that i have several hundred (400 to be exact) strains of the same virus, however the problem still appeares now and again i have tried Stuartli's solution, but to no avail.
I have checked Device Manager and the Cd-Rom controllers are not listed, in fact, when the problem arises the entry for CD-Rom is totally missing. I have now got rid of the virus using Norton 2003 with the latest update.
As For Despicable Desperado's question i have NOT added any drives, even though the system was 'Custom Built' By Jennings Computer Services of Scarborough, there was no problems with the computer, they made a good build, there on Upper Victoria Road.