I wonder if something got added to your config.sys or autoexec.bat that are messing them up. Since they are detected on the BIOS level it sure sounds like a driver / windows issue.
Take a look at your config.sys and autoexec, these can be opened with notepad (you will have to hold shift key down and 'open with' for the sys file.)
In the config.sys you may see something that looks like:
device=c:\samsung\samcd.sys /d:cd0001
In autoexec.bat something like this:
c:\windows\mscdex.exe /d:cd0001 / whatever etc.
Some of these lines may have REM infront of them. Or you may not see these lines at all as 98 is 'supposed' to handle that on install.
If you do decide to do this, when you get the screen 'starting win98' hit the escape key and note what is happening in the background. See if it loads and identifies the two cd-drives at that stage, or not.
There is probably an REM infront of the autoexec line, mscdex line.
That's fine.
If there is an REM infront of the line in your config.sys, try removing it and rebooting.
If none of these lines are there or the above didn't work, try downloading the following file here
www.sigmacomputers.on.ca/dualboot.html
CDSETUP.ZIP
Unzip it and run the cdsetup.exe. Reboot and see if the drives are back.
These are more for DOS level access to CD-ROM's but I've seen 95/98 get hosed before by config.sys / autoexec.bat settings.