So ive been having this problem, and this may need to be moved to the modded installs, but all i have is mechjeb and i dont think its whats causing the problem cause ive seen it happen without MJ installed. Essentially what happens is i hit EVA, and everything breaks.   any part windows are closed, wasd  do nothing,  escape wont do anything.  The only thing that responds is the mouse and the ability to move your camera.   The only course of action is to close it and re open ksp.   Sometimes