How large and sealed of an area are you using it in? I ask because those units have a low oxygen sensor which will shut it down if there is not enough oxygen in the space.(kinda prevents that pesky suffocation thing). Otherwise if using it in larger cold spaces, the issue is can be from the smaller tanks. As mentioned above, a larger tank can solve this, because these units have a fairly good input rate, which will cause the smaller tanks to freeze, and lower the propane temperature and evaporation rate, basically runs out of gas until the tank warms back up.
Is your Mr. Heater the model that uses two small one pound cylinders or you have the choice to hook it up to a single larger tank? if so, you must use the special filter connected to the Mr. Heater and then your hose to tank.
This happened to me and after I hooked up the filter my problem was fixed.
Mr Heater has an 800 number. They will tell you how to clean the pilot light. I have a buddy and a big buddy. I had this problem with my big buddy also. If they are stored in a dusty area you need to clean the pilot light.
Try just one new cylinder, it will run on just one, to verify a problem with the cylinders. Also it could be the pilot light, sit and watch the pilot light to see if it goes out for some reason. If it does the heater will shutdown automatically, but you already know that.
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Does the pilot light stay lit if you continually depress the control valve?
If the pilot light stays lit as long as you keep the valve depressed, then the problem is the thermocouple is bad. The pilot light makes enough electricity via the thermocouple to hold open the gas valve that feeds the burners. If the thermocouple fails to produce that electricity, the gas valve will shut down and switch off the gas flow to the whole unit.
Thermostat flame sensor. Do you see a little rod next to the pilot? That is what tells the main gas valve that the pilot is lit and it is safe to give gas. Easy swap, and you can usually just pick up a generic one.
The first thing I would do is make sure the flame sensor is clean, this is a metal rod immersed in the burner flame on the opposite side of the igniter. If too much oxidation builds up on it, it will not allow the burner to stay lit. To clean, just turn off furnace and remove flame sensor and clean with steel wool and then reinstall. If this does not solve the problem there may be a problem with the gas valve.
You must clean the pilot regularly to ensure it burns properly. Use a small can of air for cleaning computers and blow air through the pilot to remove dust and small particles that accumulate in the pilot barrel. Use several burst being that it is 2 years old and has not been blown out. THe manual references cleaning the pilot in the maintenance section.
I have a Rinnai Ventless heater hooked up to a 20 lb propane cly with a Moble home type regulator in line, and when I light it the pilot light lights and stays on. When I turn it to the heat position the pilot light go's out and that it!