Are you using Atlantis Final?
Up until Atlantis Beta2, when you added a new source & also did an automatic scan at this time, XBMC would load the nfo if it was present, but then do an internet scrape straight afterwards, thus overwriting the nfo information.
In addition & this only applies to TV Shows as far as I know...if your library was created on Beta2 or earlier, it will not recognise any new episodes using nfo's as being from the same TV show.
To fix this.....select on the TV series name, TV Information, Refresh, All episodes. It will reload the TV Show nfo & use that & all your current episodes will be removed. Now choose Scan for New Content & all your new episodes should appear. The library is now fixed for that TV Show.
Ideally when you install Atlantis Final you should recreate your library from scratch.
Cheers
Richard