regardless as I said in my previous post (which was oddly ignored, sometimes I wonder why I bother...) CCleaner would not have done anything to remove the MBR, and it also does nothing to remove either infected files or registry entries. the keys aren't "broken" to be fixed.
CCleaner scans HKEY_CLASSES_ROOT, with very minimal accesses to the other keys. It mostly looks for unused file extensions and invalid CLSID InProcServer32 references. None of the keys it accesses can harbor malware, and if it does CCleaner doesn't do anything since it still contains valid data.