Sorry for this necro but I just had the same thing when I closed that warning message thinking I only disabled the warning itself, when in fact it it will just skip closing FF forever. Weird option if one cannot reverse it. Also careless reading on my part... The advanced option "hide warning messages" was unchecked. Checked it, ran cleaner, unchecked again, ran cleaner didn't solve it.
But to anyone reading this old post for help, just uninstall en reinstall CCleaner, it's the simplest (only?) option.
