I don't know if this would be much help, but something similar happened to me when I tried to install CD Extreme (Sony's preprietory soft that came with my Sony burner) on my Win2K machine.
Basically, the registry was updated, and after that no CD drives were visible in the explorer. Uninstall did not help. The sitution was saved by the fact that install for CD Extreme showed the list of all changes done to the directories and registry. Had to go step by step and delete/edit registry classes.
It would be helpful if you could provide some info on software that you installed.