Are you saying that imporing previously exported *.reg would not bring it back to it's original state?
Importing a reg file will never remove any existing keys. It's an odd thing for a security feature to come from MS, but this is one of the few. If a reg file did provide a means of deleting keys, then someone could send you one, you open it, and you have no registry left.
re: OS reliability and co
NTx is what Windows should have been in 1996. NT4/2k/XP is far less temperamental, a far more ideal learning platform than 9x.