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.