My guess would be that the EOS switches on the flipper mechs are not closing properly when the flipper is at rest. Take a look at Vid's flipper guide, and specifically the EOS section here :
https://pinside.com/pinball/forum/topic/vids-guide-to-upgradingrebuilding-flippers#post-284674
If you're getting any power to any of the flippers, then the MPU is certainly not at fault.