So Google must have changed something in the way Chrome stores its settings/plugins, because now in the latest build (version 32) when I use CCleaner + winapp2.ini, Chrome resets itself to factory settings when you first launch it after the cleaning (it only happens once) and gives me an error message saying "Chrome could not retrieve preferences, etc" or something along those lines. It also deletes the plugins you had installed.
Chrome keeps working perfectly fine, but you have to set ALL of your settings/preference again.
In all likelihood you just need to get the latest and greatest CCleaner. Google promoted Chrome 32 to stable status a couple of days ago on 1/14, and you probably got upgraded like most of us did. In my case, I didn't have the latest and greatest CCleaner and experienced your exact same symptoms. I downloaded the newest CCleaner, did some testing, no more issues. The issue apparently arose during Chrome 32 beta testing and a CCleaner update addressed it then:
Version History
v4.09.4471 (19 Dec 2013)
- Added Google Chrome v32 cleaning and startup management.