I have a water heater that we have replaced the gas valve, replaced the ignitor, replaced the thermocoupler ( twice) have had the gas company come and check the supply - manifold 7 inches, drop out at 3.5 inches everything checks out as far as the gas company goes. The only two other things I can come up with is the venting but this heater has been just fine for the last 2 years and there has been nothing to change the arrangement. There is a furnace that uses the same exhaust vent ( after the Y connection, it goes into a common tanklike camber then out the house. The pilot will stay on and will fire up, but when the tank is heated it just goes out and then we have to start the process all over again. The filter screen underneath is so clean you could eat off it.
Could it be a air balance problem with the furnace ?