you're right, the payout counter not resetting is the problem. When that happens, you get the delta from previous pay when you get a higher pay.
on the 1088 base model, payout counter reset coil goes thru a payout counter "open at zero" switch with yellow (30) and orange/black (78-1) wires on it, and a reel mech B-3 switch with 78-1 and black/white wire 85-1.
85-1 goes to the payout counter reset coil.
the open-at-zero switch is on the ratchet/gear side of the payout counter and is operated by the reset pawl. The pawl is locked above the ratchet when the unit is reset, and when the unit steps the first time the pawl flops down on the ratchet teeth and stays there to prevent the ratchet from turning backwards as the unit steps. [oops ... it's the switch near the zero stop bumper in front of the spiral cam]
reel mech B switches are the horizontal switches on the left side of the reel mech above the coin relay. B-3 is probably the top switch in the stack.
if the win meter is resetting, then the payout counter open-at-zero switch is ok.
could also be plug connections for those wires on the reel mech or hopper unit.
schematic for the 1088 can be grabbed from
https://bingo.cdyn.com/slots/note there's lots of versions of the 1088. The plate below the handle will tell you what the full model number is (which may be just 1088). 'course, sometimes the plate got swapped onto a different game to create a paper trail. The payout counter reset circuit is likely the same on all the 1088 versions, so the base 1088 schematic would apply.