Grab a Device Manager screenshot, with the CDROM and Disk Controller trees expanded - or print a report to file - you may need to install the generic/text-only driver, in order to create a file that we can actually read.
On many systems, the BIOS reports the drives it sees, even if they are not set as AUTO - if not, try setting the drive types to AUTO, on the ports where you expect them to be - it's not usually needed, and can slow the boot slighly as it waits to check them in (especially if you AUTO a port with no drive) but it does provide a basic sanity check that the hardware is alive and responding.
If it started after you were in device manager though, it seems likely that you disturbed something there - the BIOS device check is just a handy way to confirm that they ARE at least partially ok.
Some info on the motherboard would be useful, as some are prone to driver issues.
Win98SE here.
If still stuck, we may need a forced redetect - but you need to have all required drivers ready in case it asks.
I don't think we're at that stage yet though. But I'll describe it....
From "hardware profiles", copy the the existing one, and then rename the original.
When the system is rebooted, since neither are original (the rename!), it asks which you wan't to use - choose to create new.
This forces it to redetect all hardware, and create a new "original" - from hardware profiles, delete the other two.
It's a roundabout way, but it sometimes resolves duplicated or missing devices, and cleans up any removed ones.
