Hey, i'm running the latest version of both chrome(Version 48.0.2564.103 m) & cleaner(v5.14.5493 64bit) on windows 10.
Even though i have ccleaner set to clear chrome history, it isn't working, ill reopen chrome after running ccleaner, and all the history will still be there. I'm pretty sure this just started happening after a chrome update this morning. Maybe look into it? If you need more info i could post screen shots or something.