I know some of these suggestions may sound silly and I'm sure you may have checked them already, but for what its worth...PnP enabled in the BIOS....are you positive after enabling PnP you pressed "F10" (or whatever key is right for your system) to save and exit, instead of just "esc"? In the IDE settings in the BIOS, do you "see" the CD ROM on the secondary IDE port as a secondary master? You should see both the primary master, which would be your hard drive, and the secondary master, which would be the CD ROM. If the CD ROM is NOT listed, you might check in the BIOS for a setting that would enable/disable the IDE ports....make sure that secondary IDE port is enabled. As far as testing the secondary IDE, you can verify the port works by attaching your hard drive to it...if it fires up and is detected in the BIOS then the port works. Some things in Windows to check: in device manager, highlight your IDE controller and click on properties, then the settings tab. Make sure it is the main controller or you won't see the settings tab...once you click on the settings tab, you will see a drop down box that will allow you manually enable or disable the primary, secondary, or both IDE ports...you want this set to "enable both" or "default". Lastly, in device manager, highlight the cd rom driver and click remove. Reboot, see if Windows detects it. I couldn't get my cd rom to work until after I had removed it from the device manager and then had Windows redetect it after reboot. Last thing, just curious....have you tried booting from a floppy boot disk, select "start computer with cd rom support" and then see if DOS assigns the cd rom a drive letter, like D: or F:? If a drive letter is assigned, then DOS is seeing the drive and it is more than likely just a matter of installing a fresh, correct driver so Windows will communicate with it properly.
Good luck and keep me posted on your progress...I'm running into a lot of "disappearing cd rom drives" at the help desk where I work and am compiling a list of things that I've found to work, things that don't work, etc...
Dave