Having the same problem here,
cleanonupdate in advanced settings, not working anymore since I moved in the december nightlies.
Not exactly sure which date...
I'm having a script muxing downloaded subs into a mkv for xbmc to detect the sub. (for showing if the episode has a subtitle in the skin)
I now have every episode double
Luckily I have a raspberrypi on the same mysql database still on a november build
Will attach a log when I get home....
edit:
Log here:
http://xbmclogs.com/show.php?id=99366
edit2:
I've updated to a 20131221 build (archlinux aur package 'xbmc-git'), started with a new .xbmc directory and a new mysql database.
No more problems, cleanonupdate functions as it should.
So somewhere my setup got borked.
being it my database, the git update fixed it, or a multipath wich I removed (before the update) I don't know.
I blame it on the cost of using nightlies