Running latest v5.44, installed 6/26/2018 (system rebuild). Seems that the Waterfox profile is being cleaned following the two CustomLocation1 &CustomLocation2.
The Problem is Options / Cookies are not showing the Waterfox cookies in the list so I can move the wanted ones to the Keep side. This worked fine in previous versions.
Had to use Chrome and go to these web sites and then view cookie and move them to the Keep side.
It appears to be only the Cookies list that I want to keep ( left side is blank). The cleaning of cookies is working and the "ones to Keep" are not being deleted, this is okay.
I install Firefox 61.0, opened several sites and the Cookies list ( left side) show the Firefox cookies - okay. I can "Keep" this and they seem to work for Waterfox. I never had a problem in the past with keeping Waterfox Cookies.
I always close all browsers before running CCleaner. Yes, Waterfox is closed