Ok, 99% was hyperbolic but I still think this is a connector issue as reseating them makes the problem go away almost universally and for some time. When I first started dealing with Stern games in an arcade setting I was taking troughs apart and re-pinning connectors on both older and brand new games and I never experienced a bad or cracked solder joint. I probably did this 3-4 times before I gave up and just started sticking my hand in the game every so often. I don’t see it as a jam issue either since once a game starts doing this it almost always continues until I do the push in. Obviously this is non-scientific and only based on what I feel I’m experiencing so there’s plenty of room for me to be entirely wrong. 
At the risk of being labeled a Stern apologist, I’ll just point out that the trough gets more vibration than any other area of the game. Not a great place for electronics. I change a lot more old WMS trough opto boards than I do Stern boards. Of course the WMS boards are older, but you get the idea.
Repinning the opto connectors never hurts. Preferably with the trifurcon edge connectors. Soldering the wires directly to the header pins mostly eliminates that weak point (check for cracked solder joints first). If you are a setup person for a large event, you should probably have a pair of new Stern opto boards in your tool box. If one leg on an opto cracks, that can’t be fixed without changing the opto. Easier to just throw in a new board.
Also don’t forget our old favorite: magnetized balls. I just looked at a buddy’s TWD that was acting up… the original Stern pinballs had developed slight magnetism, and that, combined with a litte dirt and typical surface scratches, provided enough friction to occasionally prevent them rolling all the way down the trough. Sometimes it’d half-eject one and he’d wind up with a trough stack or 2 balls in the lane.
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