Yes, Thunderbird has a "Compact" function but in my case it didn't work. The files must have been corrupted. Yes, Thunderbird is like OE. The deleted email is flagged as deleted but it is actually just hidden, as mentioned above. When CCleaner wiped the drive it didn't recognize these files as being deleted. When Recuva scanned the drive to recover deleted files, for some reason it did recognize these files as deleted. So, after copying any emails worth saving to a new folder, I went in to Thunderbird/Profiles/Mail and deleted all the .msf files (index files) and also any other file that was over a few KB in size. I then ran CCleaner and Recuva again and the result this time was that all the files had been wiped. And Thunderbird was working as it should. Thanks.
http://kb.mozillazine.org/Compacting_folders
http://kb.mozillazine.org/Profile_folder_-_Thunderbird