These baseball rules games are trickier and more interesting than they look. We can look at the runners on base and the hit and know exactly where the runners should end up. But consider how the game has to approach it. There are calculations to be made to determine if there's a runner on base for each base. But the order in which those calculations are made is important. Imagine there's a runner on first base and the player gets a single. The rule for 2nd, 3rd and home base is just: if there's a runner on the previous base, the next base gets the runner. If you evaluate the rule for 2nd base, the runner gets to 2nd. But if you then evaluate the rule for 3rd base, the runner gets to 3rd because there's a runner on 2nd. Similarly if you evaluate the rule for home plate last, the runner scores because there's a man on third.
Instead the game has to evaluate the bases in reverse order. First home plate looks at 3rd base on a single. Nobody there so no run scores. Then the game evaluates the rule for 3rd base. There's no one on 2nd so there will be no runner on 3rd after the single. Finally the game evaluates the rule for 2nd base, sees the runner at first base and advances it to 2nd base. So the outcome is entirely different (runner on 2nd vs. run scored) based on the order in which the bases are evaluated.
The Hit Unit is the part of the game that enforces when the rules for each base are evaluated. When you get a hit the score motor starts turning and the rules for home plate are evaluated. Then the Hit Unit takes a step and the rules for 3rd base are evaluated. Another Hit Unit step and 2nd base is evaluated. On the last step 1st base is evaluated.
Given that the Hit Unit takes a bunch of steps each time the player gets a hit it's possible that it has become loose or worn. It may be as simple as the set screws that hold the wiper disk on aren't tight and the wiper disk has some slop. Or your contacts or wipers or advance arm may be worn down. Those would be the easiest things to check for. Make sure that the Hit Unit is taking clean, crisp, precise steps and landing directly on top of the contacts every time. If that all looks good we'll have to dig a little deeper.
/Mark