The title basically states the problem. I have v 5.59 (free version). Under Custom Clean, I have Cookies checked under Edge, IE, and Firefox. (I use Firefox almost exclusively.) Yet after cleaning several times, a huge list of cookies remains in the left panel under Options > Cookies. Shouldn't all cookies have been deleted as part of the cleaning process? (I don't want to keep any of these cookies; I just want them gone.)
It can happen for mysterious reasons, and then out of nowhere can correct itself.
In the meantime something to try, although I don't know if it will work effectively:
1. Open each browser on your system, and use their own built-in cleaning tools to delete the cookies.
2. Check in CCleaner to see if they've been deleted.
In CCleaner make sure Adobe Flash Player cleaning is enabled, since there are Flash based cookies also. Warning: If you play Flash based games cleaning Adobe Flash Player will delete your game progress/saves.
Also to note that if your browser is still running (maybe in the background) then CCleaner won't be able to clean it.
If that's the case then you should get a pop-up asking if you want to close it.
But it is possible to tell it not to show the pop-up again, in which case CC will just skip cleaning the browser without asking you.
However if it does skip the browser because it's still running then it will tell you so in the results, like this where it's skipped (most of) Firefox: