Yeah, hard disks are controlled by the BIOS and removable disks (which a CD-ROM falls under) are controlled by Windows. If you had more than one removable disk than you could change the drive letters but they would still come after the hard drives. You could try making the CD-ROM the secondary master but I don't think that would work. I believe that it will always be a slave drive.

If it is just shortcuts on the desktop that point to the drive you can always change those to reflect F: now without reinstalling the porgrams.