hey guys i have experienced the same problem ,its very simple to solve it.as u know when you try to run ccleaner then a small window appears to close google chrome even though its closed and if we proceed the history from other browsers is deleted but chrome history remains,so here's the solution.
after closing the google chrome window,check for notification of chrome in hidden icons in task bar,,there u'll find an icon of chrome right click on that and click exit.
now your chrome history will be deleted along with other browsers.
u can also unmark to run chrome in background.i hope its help full
thank you.