I have installed CCleaner on both the normal and secure folder parts of my galaxy. It works fine on the normal part as I've given all permissions required, however it doesn't work on the secure folder part because it still seeks permissions even though it's been authorised already.
I can see that it picks up different things that need deleting within the secure folder than if you run it on the normal part of the phone so i do need it to work on both but I don't know how!