Had this problem on a couple of games. Check the 'ball jam' opto - it's located between #1 opto in the trough and the shooter lane to detect if there's a ball stuck there. The game is seeing the opto as closed so it keeps kicking balls out to clear the non-existent jam.
In one case is was a bad IR emitter; replaced it and no problem. The other case (and this took me forever to figure out) was a broken wire in the harness around mid-playfield. It was on the same line in the switch matrix as the ball jam opto. Figured that out when there were two other standup targets that weren't registering as well.