Hello, I am having the same issue with CC not cleaning flash history.
I am running:
Flash Build: WIN 10,1,53,64
OS: Win 7 64bit
Browsers: FF 3.6.6, Chrome 5.0.375.99 and Opera 10.60
CCleaner: v2.33.1184
If someone were to run CCleaner right now and then go over to the flash manager here and verify the history, that would be great.
http://www.macromedia.com/support/documentation/en/flashplayer/help/settings_manager07.html