Sounds like you may have the spark misaligned.
Perhaps you can substitute your own 12 volts to the gas solenoid. If the 12 volts that is getting there is not really 12 volts under load the solenoid may not be opening correctly.
Using a digital voltmeter can trick you. The 12 volts going from what looks like full voltage to a lower state and back again can happen too fast for you to see it.
A 12 volt test light at the solenoid might help sort it out by putting a real load on it.
I would also like to know if you are plugged into shoreline which would have the battery charger running. You could have poor connections along the way or right at the batteries.
Check the voltage input right at the board with your test light and meter. See if the test light goes dim for a second when it tries to light.
Your old board may be ok and the new board is just acting a bit differently.
H/R Endeavor 2008
Ford F150 toad >Full Timers
Certified Senior Electronic Technician, Telecommunications Engineer, Telecommunications repair Service Center Owner, Original owner HR 2008