I've noticed for awhile now that CCleaner runs up through the 98% very quickly. Then when it reaches that it takes forever for that last 2% to finish.
It may be an idea to post what operating system and service pack you are using and which version number of ccleaner.
Also which browser.
What does it say it is ccleaning in the window when it seems to slow down?
Could also disable all the cleaners, and then just enable them one at a time and only run one of them at a time to find out which one is causing it.