I had more comments but deleted them until I notify another member who knows a LOT more on this than I do.
First, that's an AWESOME machine!!!
Here's what I surmise...
The jackpot reservoir won't fill until the coin tube is full. Then it kicks to the jackpot and then to the cash box below.
The odd payouts might be a sticky coin slide. Or one just stuck open which might account for random payouts. The slides need to be absolutely oil free - no grease/oil should ever be added.
I'll contact member 63mini and he will have better information!