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Lets hope that is not true because if the pilot is being blown out by the fan, that means you have a cracked heat exchanger and that is a very expensive job.
It sounds like it could be a flame sensor issue.
The flame sensor Rod is a small thin steel rod that is straight or L shaped. It is usually located near the pilot igniter or the outside corners of the burner tray.
Locate it, remove it, and clean it very good with a piece of sandpaper.
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I don't think my burner has a flame sensor. I just had the whole burner out. Its a long tube with flutes on the end. The burner control valve just bolts up to the burner and the gas jet shoots gas into the burner tube which is ignited at the end by the standing pilot with the thermocouple over it. The heat exchanger is fine, the flame goes out with just the combustion fan running before the main fan turns on. I was wondering if it could be starving for gas i.e. the control valve is faulty. Do these valves get dirty or plugged and should I start with a new one there first. I am convinced the burner, heat exchanger are all fine, I checked them over pretty good. Any input you have would be appreciated. Thanks
The thermocouple is the flame sensor! Clean the Thermocouple with a piece
Clean the thermocouple with a piece of sandpaper.
In the original question I stated that I had changed the thermocouple! The problem ended up being that the control valve was starving for gas, the pressure reg. had ice in it.