This is really annoying: When Sins of a Solar Empire: Rebellion is in full screen mode, you can still move your mouse outside of the window. So if you've got a monitor to the right of the game, it prevents you from moving to the right by moving your mouse to the right side. It'll just go into the second monitor and if you click, it'll minimize the game.
This is talked about in depth on the Stardock forum but there's no solution or consistent workaround found.