The programming just tells it if it can run the heater and jet pump at the same time. You aren't getting extra voltage anywhere.
Usually old worn contacts inside the relay overheating. But it could be caused by overamping if a component, such as a shorted heater or faulty pump.
Hook up the 240v pump common wire to J32 or J25 and see if it runs correctly, or bring it to a motor shop for testing. The board damage could be from the wrong voltage to the pump, which could also damage the pump.
Check the heater terminals for continuity to ground.