No, the balls can all be in the trough to start the game or any place on the playfield, it doesn't matter. You have something else wrong, are you sure there are only three balls in the game?

John

Is the tar pit open or closed? If the diverter is closed, then there should be one ball in the tar pit ball walker and two in the trough. If the diverter is open there should not be a ball in the tar pit.

Other than that, one of the lock or trough switches might be stuck closed

I had two ball ejecting on mine and found the tar pit diverter being closed was the problem.

Did you have a chance to see if it was the lock relay for the Tar pit?

Here's an old video to a possible yet simple "fix";