Congrats on the find, took me a while as well, tho yours appears to be really nice.
I have a number of EM's(not all set up) and I've found that the EM Tech forum has a wealth of info and a better place to find your solution.
I will share that that there are at least 3 things possible and narrowing down is first step.
Is the ball kicking out of saucer? (eject coil not firing to clear and unload saucer switch)
Does this happen when you collect Silver Bonus in other saucer? (Silver Bonus Relay)
Does this happen when any other 1000 pt is scored? (1000 pt relay)
I'm not sure if there is a Stepper unit involved, if so and it's not Zero'ing out on bonus countdown( a switches closes which stops the pulsing of the 1000 pt relay) then it will also do what your saying.
And get a schematic, they are oh so helpful.