I had the same problem, but realized full screen wasn't going to work at this point in time. Also for some reason when I changed full screen in the .txt it didn't keep the changes. I had to uncheck full screen in the game itself. I then turned down the resolution slightly in order for the window to fill in my screen.
Yep - exact same problem here too. Resigned that I won't be able to rectify this anytime soon and I've been playing it in a window mode without any significant troubles.