If the problem persists thru 2 different eddy sensors, it might be a loose connection on the controller board or dirty pins in the molex connector.
Check the continuity of the wires to the controller board. Check the continuity of the contacts in the molex connector.

Sounds like a loose or worn connection somewhere.

Maybe swap controller boards around to see if the problem moves with it.

Does the game register the eddy board with a ball in switch test? It should.

Sorry, i meant the little IDC connectors. The wires get loose and weak as they get old and crispy and corroded.
I had a similar problem on my game, it ended out being loose and worn connectors.
I replaced the cables with ones from pinbits and they fit much tighter being new.
Did you check the continuity of the wires to the connector ends?

Check all of the connections with an ohm meter.

I would insure that the connections are firm and clean and proper before continuing.