Have your tried leaving CCleaner running a bit longer? has it can take a bit of time to clear everything if you have a lot of crap. I have used CCleaner for years and it has worked flawlessly.
In the mean time could you run CCleaner, and look at my below picture links and tell me if you have your CCleaner set up the same way, i.e. Which boxes do you have ticked for the various things that are applicable to you. If any of your settings (boxes that are ticked or unticked) then it might be worth you setting your CCleaner to the same has mine and then giving it another try and see if it helps matters.