I know its a pain but maybe you should install your CFBL driver board in your Indy as a test. Pretty sure the only difference is the CFBL driver board will have the flipper relay circuitry on it.

That will 100% clear your boards.

Before you do check the voltage on the driver board at test point TP8. This feeds the lamp columns. You should get around 18 VDC to ground. Just wondering if you have a high voltage there or getting some ac from the bridge rectifier. This test point comes straight off the bridge rectifier BR1.