Hi HD_Fatboy
An non-pleasing miracle "after counting down the right bonus: Then faulty counting down the left bonus". At the moment I have not an idea worth writing about.
I would like to do some tests - I believe to read in / from Your post-8: You do tests with the playfield lifted - and You manually trigger / simulate "ball rolls into the right Eject-Hole". You write "manually trigger ... then activate a second time" --- the way the pin is constructed: YOU MUST keep the switches actuated / closed - ALL THE TIME the pin is busy giving points / stepping down the bonus-ladder. Do NOT tip-on and take Your finger away --- the pin NEEDS the switches closed all the time.
You wrote "There are TWO set of switches" - Yes, see the JPG: "encircled green" is the switch to make the right Bonus-Relay to pull-in (it then stays pulling as the bonus is stepped down). When You have bonus: The situation is "as my drawn brown lines, a bit below in the JPG" - when stepping from 1 bonus down to zero bonus: The Eject-Relay must pull-in.
The second switch on the right Eject-Hole is encircled blue --- it is for: The pin MUST immediately step-up to one bonus to end the feature "ball has landed in the right Eject-Hole".
Please do testing again - park Your finger (hihi - I try to evade a joke) in the Eject hole - have the finger there until the kicker kicks Your finger - THEN take the finger away. And then write a new description "this is happening". Greetings Rolf