By zero flashes do you mean the LED is locked on?
jlbintn had a similar problem with his Callahan Mutha MPU board - anyway might be a common issue with these boards.
First of all, what voltage do you measure at TP2 (12 volts test point) on the MPU board?
And what voltages do you measure at each leg of the zener diode (VR1) on the MPU board - should be in the reset area.
One thing to note about the Mutha board is it uses a different CPU (a 6802) vs Bally that used a 6800. A key difference between the CPUs is the external clock circuitry. The 6802 uses a crystal that takes longer on power up for the clock signal to stabilise (compared to Ballys setup) meanwhile the Mutha board still uses Ballys reset circuitry that has a short time to release and let the CPU start.
The specification for the 6802 is that it takes 100 milliseconds on powerup for the crystal to start oscillating to provide the clock signal.
From previous tech support threads measuring Ballys /RESET signal release is about 4 - 10 milliseconds on power up.
In the case of this board, the CPU is coming out of reset *before* the CPU clock signal has started oscillating where best practice is that it should happen *after*. So this is potentially a problem.
What might be worth trying is delaying the /RESET signal release on powerup.
If by chance you have a 22uF capacitor, try connecting it between ground and the base leg of transistor Q1 (base leg is the middle leg) on the MPU board to further delay the reset.
Hope I'm making some sense.