Here's what I would do first. Get rid of the dos drivers loading in autoexec.bat and config.sys...they could be causing issues in Windows. Windows has built-in drivers, so it doesn't need autoexec.bat/config.sys cdrom drivers loading. Open up these two files in Notepad and put a big "REM" in front of the lines in config.sys and autoexec.bat referring to the cdrom drivers:
e.g. in config.sys,
REM DEVICEHIGH=C:\MTMCDAI.SYS /D:123 (your line will be different depending on your driver's name)
and in autoexec.bat
REM C:\WINDOWS\COMMAND\MSCDEX.EXE /D:123
People complain about "But I use DOS a lot", etc., but there is a way to get these drivers loaded for DOS
when you need them vs. every time windows boots (and I'm not talking about a floppy), so let's get rid of them. Reboot, try the cdrom's. See if the problem still exists. If it does, let's try this: Go to Windows.
Open up Regedit.exe.
Click on the HKEY_LOCAL_MACHINE key.
Now, you'll see some subfolders.
Click on the one that says "Enum"
Now, click on the one that says "SCSI"
So, you should be at HKEY_LOCAL_MACHINE\Enum\SCSI
You'll see some listings for your cdroms/cdrws. For example, here's one of mine:
HKEY_LOCAL_MACHINE\Enum\SCSI\ATAPI___CD-ROM_40MAX____4
and here's my CDRW listing:
HKEY_LOCAL_MACHINE\Enum\SCSI\PLEXTOR_CD-R___PX-W1210A1
First, see if there are any old keys listed there for devices you don't have anymore in that SCSI section.
Delete them. Close regedit and reboot. Try the cdroms. If still no good, go back to regedit.exe, and this time delete the entries for your two cdrom devices. Not to worry as they will be redetected by Windows upon the next reboot. So, delete the entries and close regedit and reboot. Windows will redetect the cdrom devices. Try using them again.
If still no go, download and run the freebie registry cleaner from Microsoft called Regclean. Here it is:
Regclean
Run it a couple of times until it tells you it hasn't found any more problems to fix.