I know this is an old post but I am having this same problem with the registry changes. I too have CounterSpy installed. I wasn't clear on what the root cause of this issue was determined to be.
It appears to me that it is probably an issue with CounterSpy and not CCleaner.
I will post these issues on CounterSpys board and see if I can resolve this issue. I will post on this board the solution if I find it or confirmation that CounterSpy is causing the problem.
Thanks for any help that is offered.