A factory reset is worth a try. Corrupted data from the CPU. Also make sure all the chips on the CPU are seated correctly. And the ribbon cable between CPU and driver board.

If it doesn't work you can swap the driver boards as a test only. The lamp matrix circuits will be the same on both. If I am correct the only difference is the flipper relay circuitry on the CFTBL driver board.

I would install the CFTBL board in the Indy though as it has known good field lamp matrix wiring. I would do this way because I think a bad board would rarely affect the field wiring but bad field wiring can defiantly cause problems on a good driver board.

I would leave all the GI, solenoids and any other non essential plugs off too.