Do all flippers do this? Or are the 2 upper ones OK?
Sounds like the fliptronics board to me, but first have you checked end of stroke switches, then that all connectors are seated correctly to all boards especially the fliptronics board.
Visually check the lower flipper coils and wiring to them.
Then may meter the power at the flipper coil to see if you are getting the correct power.
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