So no luck with your suggestion. I tried resizing/ full screen/ windowed with no new results. I went into the config file and manually set it to be at (50,50), and when I tried that it looks like the button itself is missing. Just clicking where the button should be activated the countdown, it's just invisible. In the image attached you can see part of it just below the KSP clock. http://imgur.com/gallery/b4woJKQ/new