I'm using CCleaner v2.25.1025 with Adobe Flash Player checked in the multimedia tab of CCleaner settings, and I have verified that CC does NOT remove local shared objects aka flash cookies.
Verification of non-removal can be made by going to http://www.macromedia.com/support/document..._manager07.html and viewing the visited websites.
Keep in mind that the Settings Manager that you see on the macromedia website is not an example image; it is the actual Settings Manager for your computer. You can delete all the objects by clicking "Delete All Sites" and there is a firefox add-on called 'better privacy' that will also do it but CCleaner isn't doing the job unless there is an additional setting that I'm unaware of.