Does it still eject the ball to the shooter lane? If not, check the outhole switch itself. If you have the schematic (you DO have the schematic right?) I would check the whole circuit for either a dirty or mis-adjusted switch. And where is Dr. Fury now anyway? "Paging Dr. Fury, we have a Space Mission/Odyssey patient! stat!"

Sounds like something is not completing the circuit in that ball index loop. Seriously, Steve Fury has the most knowledge of that game I have ever seen. I know he is busy with a Juke restoration, but PM him and also look for his posts here as he's been really helpful to lots of folks with this game.