What is likely happening is that the pilot flame cannot reach the thermocouple. This is usually caused by corrosion or other blockage of the gas to the area where the pilot lights. Thus resulting in a small flame or no flame on the side the thermocouple is located. Fix this by cleaning out the corrosion or other blockage in the pilot assembly. I have found that small spiders like to make their homes here which causes the blockage of the gas for the pilot. The pilot assembly has three parts to it. The ignitor electrode, the pilot light tower, and the thermocoupler. The ignitor electrode has a wire that goes from it to the push button ignitor. The pilot tower is located in the middle and has a gas line going to it from the gas valve (control knob). The thermocoupler stands next to and on the opposite side of the ignitor electrode. It also has a copper line from it to the gas valve.
Unfortunately, the Sunjoy you have, which is the same model of two I have to keep running, is difficult to service
. Parts are not readily available either so be careful when you take it apart. They do not sell the individual smaller parts in this model and therefore make you buy
To clean and service the pilot assembly, remove the screws holding the front plate on where your control knob is. Once that is removed you can see the back of the ignitor, it is black and has one wire coming from it leading up to the ignitor electrode. You will also be able to see the small gas line from the gas valve going up to the pilot tower and the small copper line from the gas valve to the thermocoupler. That assembly is what you need to get to, to clean.
You do that by removing the top canopy by removing the three screws holding it down. Once that is removed, remove the center nut on the heat exchanger (the part that heats up with all of the little holes). It is located on the top and in the center of the heat exhanger. Then remove the three screws that are located around the bottom of the heat exchanger that connects the collar to it. You should be able to remove the heat exchanger now. Tilt the whole heater
down and prop the neck on something so you can work on it.
If you look in the top you will be able to see small metal box covering the pilot assembly. This is held onto the pilot assembly with two screws. Remove those screws and carefully remove the box. Now remove the two screws that holds the pilot assembly to the collar (located on the outside of the collar). The gas and copper lines will hold it up. If you look at the pilot assembly from the top you will see one screw holding the ignitor electrode to the pilot assembly bracket. Remove that screw, unplug the wire from the ignitor and remove the ignitor electrode from the assembly. Be careful not to break this and I am having you remove it so that you do not break it.
Now remove the nut that holds the thermocoupler onto the pilot assembly bracket and pull it out of the bracket. The copper line will hold it up and be careful not to kink the copper line. Take a piece of sandpaper and clean the outside surface of the thermocoupler. Corrosion on the thermocoupler could cause it to fail which will cause the pilot not to stay lit. I have not had one do that yet but it could happen.
Now, remove the gas line from the bottom of the pilot tower so that the tower and bracket are in your hands. Put it down and put the heater back up straight. Hook up your gas and turn the gas on. Now, press the control knob on the pilot setting to make sure you have gas coming out of the gas line that feeds the pilot. You should be able to hear, feel and smell it. If not you have a regulator problem or an empty tank. Turn off your gas, remove it from the heater and tilt the heater back down.
Take your pilot assembly, you will see a circular top to the pilot tower that is held down with really small metal ears. Carefully bend the ears back with a needle nose pliers so that you can bend the top of the tower back. Only bend it back far enough to clean the inside of it with a bent wire and compressed air or something. If you look on the lower side of the bracket, above where the gas line is threaded on you will see a hole that goes all the way through the assembly. This hole regulates the pilot gas pressure and allows the gas to mix with the air before it burns. Make sure that hole is clear of debris and take wire or something and thread it through the hole up through the top side of the tower.
When you have it clean, reconnect the gas line, thermocoupler and ignitor electrode. Once reconnected and before screwing the assembly back to the collar, I set the heater back up right and reconnect the gas. I then light the pilot to make certain you have a good strong pilot light generously touching the thermocoupler. The pilot should stay lit after holding the button in for a few seconds. Do not turn the heater on past the pilot area without the heat exchanger on or you might singe your hair. If the pilot works the way it is supposed to, turn it off, disconnect your gas, tilt the heater back down and reassemble it following the intructions in the opposite manner.