Did you run the switch test to check for closed switches with the balls removed?

If you are sure the outhole and trough switches are good, then make sure the switches in the saucers aren't stuck shut or you have a shorted cap on one of the switches causing havoc with the switch matrix.

If it is the Fathom you recently acquired that had been sitting for 12 years I'd suggest the fun task of re-pinning the connectors -- starting with those that connect to the MPU.

Initially I had an issue with mine in that the MPU was not always getting a clear reading/signal from the trough switches -- the "double playfield score" insert would light and flash but nothing else would register on the game. Re-pinning the connectors fixed the problem.

Sometimes I try to cheat and get by without re-pinning. . . but I usually give in, devote some time to it, and it seems to fix a lot of these quirky issues.

Fathom will look dead after the 7th flash if it does not see all the ball trough switches closed. If you have a solenoid data problem it may not be able to stage the balls in the trough properly... ie the 3 jam up in the outhole instead of sitting on each switch.

Even when it looks dead after flash 7 it will go into test mode. With test mode check all the switches, specially the ball trough and locks. Check the solenoids all fire. Missing solenoids check MPU J4. Missing entire row or column of switch matrix check J2/J3 depending if cabinet or playfield issue. It is a lot easier to tell whats going on in the trough if you take the apron off.

Connectors in Bally games are usually a mess if original. Specially game that spent time in not so great storage. It sucks to repin plugs, but a lot of times it just needs done.