If you have the old board out, look over all of the solder connections real good with a magnifying lens. I have repaired several boards that had intermittent operation over the years due to cracked connections. My own pool heater had this as a problem. It would start fine and run for about 10 min then shut down and not restart until I cycled the power. Sometimes it would not fire up until some time had passed. I was trying to figure out what was wrong with it one day and had the top off of the unit. While the top was off, it ran fine for 3 hours. when I put the lid back on, it shut down about 8-10 min later. Thinking I had a bad relay on the board, I pulled it out and was looking up the numbers for the relays on the board when I noticed the power input moldex on the board was not soldered on too well (cracks around all 5 pins). Might be worth a shot to look.
