If you power up the game with only three balls installed (and disregard the "PINBALL MISSING" message), does Outer Space finish all right?
My memory of the nuances of Junkyard's rules is a bit hazy, but I believe that it normally keeps one ball staged in the popper near the left inlane. If I'm right on that, then the end of Outer Space would be the only time when all four balls are normally in the trough. And if that's the case, and if the game works all right with three balls installed, then all signs point to a problem with the fourth trough opto.