Okay! I think I know what happens then! The game picks from a list of resolutions supported by the screen, and I assume what happens is that it picks the resolution with the highest "height", which would make sense if you can rotate the screen. I assume the game picks the "rotated" version of your screen. :) I will see if I can change this to widest "width" instead. Thanks!
Hey! We just released a small maintenance update (0.6.8.4d ) and this was one of the bugs we attempted to sort out. The algorithm will no longer choose the last of possible resolutions, but look through all and pick the one with the largest width. If you have time to test that it works it would be greatly appreciated! We don't have screens that can rotate ourselves. :P