I've just found/installed Media Companion, it looks right up my street.
I've ran into the same problem and I think I know whats going on (possibly maybe). My tv show folder/file structure is like this...
\TV\Battlestar Galactica\Season x\xx - Episode 1.avi
To get XBMC to scrape my tv shows correctly I had to add the following to my advancedsettings.xml file under the tvshowmatching tag.
It appears that Media Companion is using the default method that XBMC uses to find tv shows for scraping.
If this is the case, is it possible to add the new search method?
Please note I've been at this for about 15 minutes, I could be seriously wrong lol :p