Usually problems like that are coming from connectors pins, diodes, contact adjustment.
Look like you make a playfield swap, very old diodes or wires that broke during the swap is common. Check carefully the drop target assembly and you will find it.

Bad relay under the playfield possibly. It switches between some coils, so if it's not working you'll get flaky behavior.

Did you ever solve this?
-mof

I had a similar problem with my Fathom. I solved the issues by swapping in a known working "Solenoid Expander Board" under the playfield. Sounds like the OP was on the right path.

"Solenoid Expander Board" -- what is its role?
-mof

The decoder on the solenoid driver board can only decode 16 addresses, one of which does not control any solenoids and is used to signal an inactive state. This leaves 15 solenoids available for use. As games became more complex and a need for more than 15 solenoids arose, Bally overcame this limitation by using the SEB to add anywhere from 1-15 coils using a single lamp address as a bank select. Lamp off - coils 1-15 selected, lamp on - coils 16-30 selected. Due to the lag in activating the SEB relay, quick react solenoids are on the "lamp off" bank and other coils like saucers, target resets and the outhole, which don't need to be fast are on the "lamp on" bank.

The solenoid driver board doesn't do "banks". It thinks there are 15 solenoids in the machine. Period. That's why wrong coils will fire if the SEB lamp burns out, connectors fail or the relay goes bad. So if you have a machine with a SEB and weird things are happening with the coils it's usually the first thing to check.

I already installed a new "red" SEB a few years ago, and it cleared up some issue (I forget what)

Here's the problem I am now having:

1. Play balls 1-2-3 no problem on rest of playfield
2. Shoot any ball into cave, and it always registers, "mermaids trapped" (switch 5 seems good) -- BUT -- sometimes it fails to raise 3 targets and say "dive again" and feed a new ball.

Clues:

1. sometimes right lower flipper has chatter
2. sometimes 2x scoring mode happens randomly?
3. last night I pressed the right flipper switch lug with the wire on it, and I saw "3" in switch test -- which is the top trough switch... WTF

-mof

Got some tips/ideas already here: https://pinside.com/pinball/forum/topic/fathom-owners-club/page/9#post-4460869

https://pinside.com/pinball/forum/topic/bally-fathom-shop-job#post-1716042

My past self already solved this, I'll go check in with him and see what's up

https://pinside.com/pinball/forum/topic/tech-fathom-cave-saucer-3-green-targets-dont-rise-after-locking-ball

Ok - so if I hold the switch down with a pencil - it works -- very strange, I suppose it is the switch -- will have to take a closer look -- tougher working on components way up there - especially when PF is on the hinge.

-mof

I cleaned the switch, and bent it up a little. It's all fixed for now -- but I still don't get how...