i have the same or similar problem, ccleaner 2.26.1050, win7 x64 ultimate
if firefox/mozilla is set to delete cookies in 'applications', it deletes ALL cookies, including the ones i said not to delete in the options, if i untick the firefox cookies box in applications, it does not delete ANY cookies.
sometimes no firefox cookies show up after a deletion, then suddenly all are listed. this just happened to me again, was showing only three cookies in options in left panel. ticked 'cookies' in applications, now shows 146 cookies. if i untick the cookies in applications for firefox, the list goes back to three (for ie). in any case, the cookies i selected to keep are also deleted.
edited:
OK, figured it out cookies only appear in the left cookie options box if you have ticked the cookies box for the respective browser in the windows/appliction settings. you can then move the keepers to the right (i found more of my keepers duplicated in the left list but with www. prefixes, re-added them on the right & they did not get deleted next run.)
i would have expected ALL cookies to appear in the left box no matter what the settings in the windows/application section.