To do your due diligence, I would ask Raypak what the service tech should be checking and see if the service tech does all that Raypak asks of them. This is site is pretty DIY, but there is also much to be cautious with when dealing with a gas pool heater. If you are any bit uncomfortable or unsure on checking the heat out, don't!
If you are proceed with caution.
Things to check:
- Unitherm Governor Operation - mixing valve used to maintain a constant temp in the heat exchanger as long as there is enough flow
- Internal Automatic Bypass Valve
- is water going through in the correct direction (manual indicated that it can be reversed but the heater need to be reconfigured)
- check the high limit temp switches, they should cut out at 135°F
- Gas pressure (I would leave this to a pro unless you are one yourself). The manual only suggests that sooting could happen if the gas pressure is to high.
If the gas pressure were to high and the Unitherm Governor and internal automatic bypass and temp limit switches were not working then you could have the issue you are seeing. The temp limit switches will cut the gas flow if the 135 limit is reached. If the water flow were to low the limit switches should kick in and prevent this. If the Unitherm Governor and/or Internal Automatic Bypass Valve isn't working it could limit the flow in the heat exchanger cause this issue.
The Unitherm Governor and Internal Automatic Bypass Valve can easily be messed up with bad water chemistry. Based on the a Raypak manual of what they do and how they work, I think I would make sure these are checked at the beginning of the season and maybe during the season depending on usage. To high or to low of water temperature can cause deposits that mess up the heat exchanger, Unitherm Governor and/or Internal Automatic Bypass Valve. If you are constanting hitting the limit switches because of low water flow it will eventually cause deposits to form on the Unitherm Governor and/or Internal Automatic Bypass Valve and they will not work as intended, it just a matter of time.
if you want to eliminate the issue of melting the header you can get copper-nickel ones, but this is likely going to be a bandaid and just take longer to fail. The likely cause is water quality and/or low water flow.
The heater works like you are driving a car where the throttle is an on/off switch, you are either off the gas or have it to the floor. The temp limit switches are like a speedometer that cut the gas when a speed is reached. The Unitherm Governor and/or Internal Automatic Bypass Valve are there to limit how often the throttle is turned on and off. They do this by controlling how much water goes through the heat exchanger or if bypasses it.
Since you have variable speed pump, I would do some testing to determine what is the minimum speed it can run at without causing the to gas valve to cycle and have it on continuous when the pool is at the desired temp or close to it. I would then make sure the pump is at the speed or more when the heater is on. The next thing to determine is if there is to much flow with all your pumps or above a certain speed that would overwhelm the bypass cause to much water to go through the heat exchanger causing it to drop below a certain temp (it's in the manual). Either limit the speed of the pump or pumps and/or install an external bypass to prevent this.