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Clean burner tube with proper brush, such as long spring type for bar-b-Q burner tube that are available at most hardware stores, and make sure you have new burner tube aligned properly (straight on) with brass orifice on gas control. Then be sure to adjust air shutter for nice blue flame, with little orange at tip. Do not give so much air that flame roars or jumps off the end of the burner tube. Too many people think more air, less fuel, but actually, when flame roaring and jumping off end of tube, the heat passes through faster and it takes longer to heat the water inside the tank. Like I said, only enough air to have quiet, steady blue flame. If your not giving it enough air, you'll see dark soot on trailer above water heater, which indicates burning too rich, need more air, or perhaps pilot is partially plugged. Pilot flame should also be blue, not yellow/orange. Small air intake hole on side of fitting just before pilot tube can get spider web, or debris in it as well. Use air to blow that out or a piece of wire like a paper-clip to clean inside that hole.
Make sure thermocouple tip is seated inside the burner flame. Make sure thermocouple is not overtightened. Finger-tight + 1/4 turn. If the pilot lights, then ECO energy cut off is not tripped, but gas control valve might be bad. Check color of pilot flame: it should be strong and clear blue. If pilot flame is weak, or color of flame is yellow-orange: Clean pilot orifice and burner and combustion parts on yearly basis. Clean air intake screen if applicable. Increase air supply to water heater. Open a window and see what happens. Check for adequate draft going up chimney using match under vent hood to see if smoke drafts immediately upwards. Bleed air out of gas line. Check gas pressure.
You are correct, there should be no flame after it shuts off. Pull the + wire off at contacts as well and see if flame remains, if it does, the gas valve is faulty (leaking by) and should be replaced.
Remove your entire pilot assembly from the heater and gas valve. Remove the aluminum gas line that feeds the pilot assembly. There is a small orifice inside the pilot assembly that may or may not fall out when you take the line off. If it does not fall out remove it and be sure that the very small holes in the top of it are clear. It sounds to me like even though the flame is blue and in contact with the thermo-couple, when the main flame turns off it causes the pilot flame to wave away from the thermo-couple thus shutting it down due to a weak pilot. I have run into this several times and should do the trick.
Make sure that the water is not coming from the drain valve, the relief valve or some top fitting and running down the insulation inside the visible outer skin of the heater.
If it is truly a bottom leak, which is common when the heater fails, if the leak is getting on the flame or pilot, you should shut it off. If the water creates an unacceptable situation, for example, leaking on a finished floor, shut the water off.
If the water is leaking slowly and the flame is not being wet down, you can call a plumber and use the tank on an emergency basis.
You will need to replace thermocouple or you might get by for awile by cleaning old one by lightly sanding tip and making sure it is positioned in center of pilot flame. When you light pilot hold down on pilot button until you can see the tip of thermocouple glo red. If after cleaning the pilot won't stay lit after you release button then you need to replace it. Remove thermocouplefrom gas valve and pull back on it to remove it from pilot assembly. You can buy universal replacements at most hardware stores. Try to get one at least as long as the old one. Good luck.Ihope this helps you. Thanks.
Usual problems are:. Bad thermocouple, Bad vent, blowing pilot outl. Too small of pilot flame. Low gas pressure Leaking water heater, dripping on pilot. Bad gas valve. If your water heater is more than 8 years old and the gas valve is bad, I would replace the water heater. IF you decide to replace the pilot or the gas vavle, be sure to mount pilot exactly as is was designed. If you replace gas valve get an exact replacment or a "listed" replacement. If you'rd doing this and it's older, replace the temperature/relief vavle also. Water heaters can be very dangeroius if not properly repaired/maintained.
Thermo coupler may be defective. it controls the main gas valve by closing main if pilot is out. make sure thermo coupler bulb is positioned over and near tip of pilot flame, but not in the flame. Thermo couplers are inexpensive and easy to change out.
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