I think you should contact the Nero people, explain that you have two versions of their software and need to be able to make it work with both drives. Maybe they can give you a new serial number with both drives enabled for 5.5? If not, maybe a discount on a 6.0 Upgrade that will support both drives.
I looked at the Clean Product Info, they do have a support forum and ask a qeuestion page and a knowledge base. Have you tried any of those options? Maybe someone has the same problem as you for Windows 2000 and they already fixed it?
Good luck.