You should be able to disable the Virtual CloneDrive by right clicking on the CloneCD tray icon, selecting "Virtual CloneDrive" and then setting the number of drives to "Disabled".
I think you will have to reboot your computer for it to register the changes.
The thing that bugs me is that you can't set the starting letter for your virtual drives.
I have a primary IDE drive that I boot from (C
,
a SCSI hard drive that I burn CDs from (D
,
a CD ROM (R: for reader),
a CD-R (W: for writer),
and a zip drive (Z: for zip).
I set up my CD drives with higher letters so they don't get pushed around if I add more hard drives in the future.
I have a USB removable hard drive that I would like to make U: but windows 2000 won't let me. So that normally shows up as E:. It usually works good.
The problem is that now virtual clonedrive loads up first (if it's not disabled) and takes E: and bumps my portable HD to F:.
I'd like to have a CloneCD setting that lets me specify which letter to start with when adding virtual drives. I would probably start somewhere in the middle of the alphabet like "I:".