I agree this is bothersome. The reason that this happens when you pause the game is that the mouse pointer is "warped" to the middle of the screen whenever gameplay is going on. This ensures that mouse movement controls will work properly.
Actually now that I think about it, I'm not 100% sure we need this anymore. Joe, what do you think?
I had a sort of hack fix that remembered the mouse position before the game started, and then when the game was paused or left it would put the mouse pointer back in that position. However there were problems with this fix that caused other issues so I removed it before the release (it didn't really fix the problem anyway).
I think a better solution might be to start the game with the mouse pointer in one of the corners of the game screen. Then maybe I can find an improved way to put the mouse back where it was when the game is paused.
Yes, you can use the joystick to go to the Pause menu in the game. Just assign a joystick button to the Pause control in Options -> Controls -> Assign Controls -> Game Controls.
Thanks for asking me to fix this up, I too like to play on my couch sometimes but haven't in a while, so I haven't had the opportunity to be bothered by it not working right. There might be one or two other things that require the keyboard...for instance, to cancel adding a new control, you must press the Escape key. Now that I think about it, I could just make it time out if nothing happens after 5 seconds.
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