Hi Adam, I think you will need to reproduce the issue I was having with XBox 360 controller and Windows version in order to fix it. When you try and customize the joystick settings the user interface feels very broken as if you are using some kind of busy loop to wait for next input.
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I gave up trying to configure xbox controller on windows version to use DPad and A button so that was a bit frustrating.
<edit> OK managed to configure joystick second time but there is something buggy with the way you program the controls.
Also the main menu timeout could reset on input so help screen does not appear when player is using main menu.