My TB 3.8 is acting crazy too, but the shaders do work. I got that for a few seconds too right after checking the "shaders" box, but after a while, it worked all fine and had shaders on. I'd wager it's something similar to games showing a blank (although usually black, but that's just cosmetics) screen after changing the display options. The difference here is that toggling shaders is the only major option in the game, so you don't get it for the smaller ones, I'd guess.
so in short, my advice: the good ol' wait for a while.