Rottendog and my Jungle Lord didn't work well together either, but in that case the game was buggy for a short while and then just wouldn't boot at all, so I don't think your issue is the board in this case.

Take my thoughts with a grain of salt, still rookie here, but:

I think a backwards diode would definitely cause your coil not to work. My understanding of coils (could be wrong) is that both ends are supplied voltage. So there's no difference in voltage and therefore no electromagnetic activity. When a coil is to fire, one end is grounded and now there is a voltage difference. If a diode were pointing the wrong way, it would allow both ends to remain at the same voltage, therefore the coil would not fire.

Another possibility is that the mechanisms are gummed up with grease and dirt. I had target banks that would not reset in my Taxi that I disassembled and cleaned and now they are perfect. I even have one in my JL that I plan to do this to this weekend.

What happens if you manually reset the bank and then manually hit the targets. Do they drop quickly into place, or do they move slowly and resist dropping?