Adjusted so they are 'barely protruding' is simply not correct. You shouldn't really need to adjust the buttons to rest lower. They are designed to be all the way up and the switch adjusted so the top blade is pressing up *just* enough to keep the button all the way up, and second blade is not gapped too much or too little. With them sticking up only partially they can't get the same switch closure 'wipe' and closure time that they were meant to all the way up and you could end up with an issue like this where the closure time and stroke are insufficient. They already have very little closure time as it is. This is all assuming the buttons are in fact totally cleaned in their bushings and are not sticky in the pf holes.

<<I have tried making sure the NC in the 50 Pt circuit on the score motor is making clean contact>>

Do you mean you actually cleaned that switch, or just checked that it is making adequate contact when opening/closing? That one could be well-worn causing intermittent contact and need cleaning if you haven't yet. And adjusted for adequate closure if it is over-gapped, also tighten the switch stack screws on it first.