From device manager, delete both drives, and the IDE controller that they are connected to.
Reboot, and allow Windows to re-install the drivers for the IDE controller and the CD drive.
You may need/want to download and install the latest drivers for the chipset on your motherboard.
If a name brand PC, check the mfgs web site.
If not, check www.motherboards.org or www.wimsbios.com to find who's motherboard you have, and links to motherboard mfgs.
You may have a line in Autoexec.bat,or config.sys (use either msconfig or sysedit to check these files) that is assigning a high letter for the drive in DOS mode, and Windows is finding the drive in Windows.
Unless you need DOS mode access to the CD drive, you DO NOT need to install the driver that came with the CD drive.
Chas