I have this problem just now. As my computer was installing some software a power failure occured and the computer was shut down. After I booted it, win 98se showed a blue message (not BSOD) about some "child" IDE controllers that are corrupt.
Anyway, Windows eventually booted but now has no CD Roms, none of the 2 that are installed.
So I went to Device Manager to check and there are 2 yellow exclamation marks on the Primary & Secondary IDE controllers (single Fifo) under the "Hard Didk COntrollers" branch.
I tried removing the parent branch and rebooting and reinstalling but that did not help at all.
Also, Win98 does not shut down anymore but rather hangs there in the "Windows is Shutting Down" screen... what gives in this case? It used to shut down OK before the power failure occured.