I'm having some weird issues since upgrading to El Capitan as well. All windowed mode resolutions are way off, half pushed off the screen and the mouse doesn't visually line up with where the cursor is active in the game. It does work okay full screen, but feels more sluggish than before. And then I started having weird keyboard issues... like it was completely remapped and then not working and lagging really bad. The keyboard issue may be unrelated, but only happened after logging into the game, and hasn't recurred again since restarting after logging in.