Just FYI, not everything ccleaner finds is really a major problem, broken links for example are simply skipped when encountered but it still helps a microsecond to just not have them there.
Is there and chance it is out of space?
and have you run a
chkdsk c: /f to verify there are no drive issues?
One other thought that came to mind is libraries set up with criss-crossing paths. Like by default My Music has a library link under My Documents, if you were to create a library link under My Music which pointed to My Documents it can cause an infinite recursion problem. If you created any library links you want to make sure they are not chained this way.
Other than that I'm afraid I am at a loss and can only recommend trying other back-up software that is available, for example Macrium Reflect Free which is listed in our
Freeware DB.