Hi. CCleaner usually cleans Firefox files from C:\Users\XXX\AppData\Roaming\Mozilla\Firefox\Profiles.
But if you decide to move this folder onto another partition of your hard drive using the profilemanager of Firefox (execute: firefox.exe --profilemanager) in order to access your profile from several OS (eg vista, xp and unix), this folder is no longer cleaned... until you do it yourself with Firefox.
It could be a good idea to look at the C:\Users\XXX\AppData\Roaming\Mozilla\Firefox\Profiles.ini file which contains the new profile location before cleaning
thanks!