When you compact files you are either missing files or not compacting properly. I tested using a program called Speedyfox from Crystalidea (download here - http://www.crystalidea.com/speedyfox ).
Run CCleaner compact, then run Speedfox. You will also see that even after CCleaner compact Speedfox finds even more space to compact. SpeedyFox tells you all the filenames that it is compacting but I cannot tell what CCleaner is doing.
This appears to be true with Thunderbird also.