Isn’t it odd that registry cleaners find new problems every time you run it? Bear in mind that many registry keys are dependent on others. Sometimes this relationship is nested deep in the hierarchy. The registry cleaner finds the lowest entry in the chain which appears to be invalid and deletes it. Next time you run the registry cleaner it finds the next entry in the chain which is now invalid and deletes it. This continues every time you run the registry cleaner until the keys for that program are completely messed up.
Some registry cleaner programs highlight simple orphaned keys, i.e. deleted and renamed files, giving the impression they have found many serious problems. Others concentrate on the HKEY_CURRENT_USER hive which relates to a specific user, which, in some circumstances, can survive being corrupted as a new account can be created and the old one deleted. In my opinion, these cleaners must have a backup facility in order to correct any keys removed erroneously and they should only be used by someone experienced with registry keys/structures.