a single point of failure for all the low pays is the "open at 50" carriage switch on the payout counter.
that switch is on the wiper side of the unit and has a grey/yellow wire on one of the blades. It's vertical and in the lower-left corner of the unit. The mating blade connects to the F trace. That switch should open after 50 or so steps of the unit. Since it's the carriage pushing the blades, the exact step the switch opens will be +/- a few steps due to slop in the carriage movement.
the schem for the 1090-37 is on
https://bingo.cdyn.com/slots/if you can post pictures of the payout counter, that's be great. Most 1090's do not have the carriage switch. If size is an issue, email highest possible resolution pics of whatever you like to slotpics@cdyn.com and I'll add them to the above. Pics of entire game front and the internals are always helpful.