You're going to have to go through the settings and programming to make sure that everything is set correctly.
As a short term fix you can return the heater to manual control and leave the Aqualink out of the picture.
Contact Jandy. If you're online, they can link into your account and help you with the programming.
Tell them that you have narrowed it down to the programming and ask them to go in and take a look.
Did you verify that the two wires are connected to the aqualink circuit board in the correct place as indicated by the drawing on the inside of the door?
You already had a service technician come out. What was their diagnosis?
If the heater is getting power, I think that you need to check the programming and all of the wiring.
Do you have a picture of the aqualink where the heater wires connect?