They do show up, they just won't show up in the tv shows without the metadata. You can find the files under video --> Files. If you want them to show up in the tv shows tab, you either need to find the metadata or make your own meta data file.
Check tvdb to see if the tv show is listed. If it is, then you can try to rename the folder to get the metadata. It can be pretty picky sometimes...like I had Venture Brothers and media center master couldn't find it at tvdb, but when I renamed to The Venture Bros., it was found.
And you might as well get the skin you want to use and do the setup on that instead of confluence. XBMC has a lot of user generated stuff, like apps, skins etc. Which is great except that not everything works with everything else. So if you get confluence set up how you like, you might find problems when you switch to another skin. I had some issues with aeon mq3 that I didn't have with confluence or aeon nox. When you try to run it as a fullscreen window instead of true fullscreen, sometimes exiting menus causes a lock up...if I don't use fullscreen window some of my emulators don't work. So I just use nox now, but dang it, I don't know why the skin creator would disable the mouse for it rather than give users the option of using mouse or keyboard, or remote. One of the reasons I like watching movies on my computer is to have mouse control and be able to skip to a certain point by just pointing and clicking instead of having to FF through a movie.