Alan, I installed PM and it automatically goes into a different program folder, but apparently CCleaner finds it. I left FF installed too. I ran CCleaner and it cleaned up all my cookies.
I then used PM exclusively until I had a substantial amount of cookies generated. Ran CCleaner again and it cleaned them all up. It showed up as FF files cleaned in the list, but they must have lived in PM because I didn't use FF.
Both browsers have separate directories also for the profile folders so CCleaner must be looking beyond the FF folder.
I really like PM a lot. Had a few quirky issues that I have all pretty much resolved, but it's worth it. The only issue I have left is getting MozBackup to find PM Profiles folder, but I'm on the case and am pretty sure I can get that to work too. BTW PM has a great migration tool to keep the same setups, bookmarks and extensions all loaded into PM painlessly.
Floyd