I am having the same problem after upgrade to Sierra. Refer to attached screen shots.
(1) Before supposed cleaning: 309 MB to clean ("Analysis")
(2) After supposed cleaning: 0.1 mb cleaned ("Cleaning Complete")
(3) After supposed cleaning + run analysis again: still 309 MB to clean ("Analysis")
Appears CCleaner has stopped working after Mac OS X Sierra upgrade.
As an aside, this forum seems extra difficult to use on multiple levels. (Maybe you do not want feedback when your software is broken?)
Before Supposed Cleaning 2016-10-01 SAT.tiff
CCleaner Cleaning Complete 2016-10-01 SAT.tiff
CCleaner 2016-10-01 SAT Analysis 2 after supposed cleaning.tiff