I dealt with a similiar issue like this a couple of days ago when a friend of mine installed a USB Flash card reader, the Flash card reader would take the CD-ROM's drive letters and the CD-ROM's would disappear in his Win98 machine.
Fixed it by using TweakUI, I can't remember the exact tab, but it's where all the drives are listed A-Z, I noticed his CD-ROM's got bumped to say K & L, but they were unchecked, I re-checked them and they showed up again after a reboot.
I also remember a thread around here about fixing that issue, I'll try to find it.
Edit: For some reason I can't find squat on it!
See if any of these help.
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