Interesting. Go into switch test (ball in hand, all targets up) and see what number the machine reports back for that switch.

If the switch is scanned by the cpu, and sees a closure, the cpu goes into a subroutine that tells it what to do with that closure. In this case, fire the saucer, score the value of that switch.
Seems to be an impossibility not to score if it fires the saucer.
But stanger things have happened.
A line of code went missing?

What are your switch settings for # 14 and 15 on your MPU? They govern behavior for that saucer.

Once I had a repairjob here where the saucer scored the points but didn't kickout the ball
Everything tested okay, from decoder to coil...
It took me some time before I realised that the MPU had the wrong eproms on it.

But thats an opposite situation

@Zombywoof
The ball always kicks out the saucer endependant of the score settings.
Please think first and only when you are really sure get your keyboard.

@Validpowerdetect
You are correct in this but remember that the MPU will never boot if you chance only one single bit of the code.
There are No "lines" in this software, it was not assembled, it was all directly written in 6800 machinecode

The OP reports that the saucer kicks out the ball but does not score any points. Isn't that exactly what the manual says will happen for that saucer if 14 is off and 15 is on? Maybe I have misread that, but I was just trying to help.