New logic board and sensors don't fix it. What next?

I have two garage doors that had a lightning power surge. I replaced the logic board and safety sensors on both. It fixed one, but the other still does not work. I have swapped boards and it is not a faulty circuit board. When I try to set the travel limits, the motor only works for about one second when I try to program the up travel. It then makes me try to program the down travel. Again, the motor stops after about one second. If I pulse the travel buttons for less than a second, I can push it repeatedly, but if I hold it down, it trips. Any ideas about what is causing this and what is the next part to check? 

Thank you!

What brand and model number do you have?
You say you replaced the safety sensors on both doors? Do you mean the infrared eyes that are supposed to be located approximately 6" from the bottom of the door?
How far apart are the doors from each other?
Are the LEDs lit up on both sets of sensors?
Are the LEDs the same color on each door or are they two different colors? (green, amber) Residential sensors are two colors and commercial sensors are the same color

A good possibility is what is called "Cross-talk", where one of the sensors is picking up signal from a sensor on the other door. Swapping the pair on the offending door around may alleviate the issue..