Delete and re-install the drivers for the IDE controller. If you changed the motherboard, Windows may not use the correct drivers. Also check that the 16-bit compatibility mode for drive access is not used, as in that case Windows will only see optical drives when real-mode drivers are loaded in DOS.

1REGEDIT4
2
3[HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\VxD\IOS]
4"NoIDE"=hex:00
5

Getting rid of "NoIDE" registry key will fix it f it exists at the HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\VxD\IOS location.

I had similar problem and it ended up being that the optical drives simply didn't like each other (At least didn't like being in a same ide cable even if they were correctly configured to be master and slave). Both worked alone and when I switched the second drive with different optical drive both drives suddenly appeared in win98. In dos I didn't have any problems accessing them with dos driver and mscdex.

Just had this happen on an IC7-G. I'm not 100% sure what the problem actually was, but it had something to do with the way the ICH5R and the Silicon Image SATA controller can appear as legacy IDE and whether they share IDE channels 1/2 or enumerate as 3/4. The BIOS lets you choose from a couple of options. With various configurations, the BIOS would show my IDE and SATA optical drives, but Windows would only detect one or the other despite having the drivers for both controllers installed. I'unno. Finally got a combo Windows XP liked, so I let it be. Moral: Try them on different channels if you can.

I removed my unused PCI Ultra66 ATA controller (as the board has onboard ATA-100) and I thought that would have fixed it but the optical drives still aren't showing up under My Computer.

EDIT: turned out I just needed chipset drivers and all was well. That was surprisingly easy.