[bagofcrap24]

Just tried #0807 and I'm still having problems fully cleaning the library. Something I'd didn't mention the first time around is that I'm using a MySQL db and to make sure there wasn't any problems carrying over from 88 I dropped all the old databases before upgrading to #0807 and scanned all my tv shows back to the library. After doing so I marked all 20 episodes in that series watched from Kodi and deleted the episodes from the server. I then used texturecache vclean to clean the library and the episodes themselves were removed from the library, but the top level series was not. I also queried both the episode and tvshow views in the database for the name of the series and it did not appear in the episode view but did appear in the tvshow view. The only thing I've changed is going from #0804 to now #0807. Any other suggestions would be great.

You say you have deleted the episodes but does the TV show directory still remain. I only say because I think I have seen this behavior in the windows Gotham builds for a long time.
My example is with breaking bad.
I have the folder for breaking bad, it is completely empty. No season folders or anything but as long as that named folder is there I will get the top level entry in xbmc