It seems to be happening mostly with Firefox & Chrome Internet Cache.
When I click analyze, the correct number of files appear that should be cleaned out of those two entries, but when I run it, it only cleans a portion of them. Then, if I click analyze right after it finishes cleaning, it will show the correct number of entries remaining (a small portion of what it should have cleaned the first time around). I clean again, and the same problem reoccurs. I'll have to do 3 or 4 consecutive cleans to clear out all the internet cache files.