Hmmm, I set it to default to 22 civs in the XML for the scoreboard. I wonder what graphics settings you have to have that go off the screen. Or maybe I set that number wrong in the XML. Well anyway that's not important, just pondering.
This is simple to fix, Press Ctrl + Alt + O to access the BUG options. In the scoreboard tab, set the number of max civs to be displayed in the scoreboard to something small enough not to go off your screen. The bottom of the scoreboard will then have a slider bar so that you can scroll through the civ list in the scorboard by moving the slider.