1) If your water heater plugs into outlet, then electronic gas controls are susceptible to power surge. and reversed outlet polarity, and undervoltage at outlet, lack of ground wire continuity between ground plug and manifold tube connected to bottom of gas control valve.
2) If sediment builds up inside tank, it will cover thermostat probe and cause probe to malfunction.
Tank can have sediment flakes build-up and still drain perfectly clean water.
3) There are 2 general types of Honeywell electronic gas controls valves installed on Whirlpool heaters.http://waterheatertimer.org/How-to-troubleshoot-gas-water-heater.html#intellivent
The gas control for atmospheric water heater (passive vent at top of heater) is modular, and is not always removed from tank when replaced.
The other gas control for power vent models is removed completely.
4) Remove thermostat from tank to reveal 3/4" opening.
Look inside tank.
To remove sediment flakes: Tape assorted plastic pipes and tubes to shop vac hose and see if flakes can be removed. And remove drain valve.http://waterheatertimer.org/Clean-sediment-out-of-water-heater.html
5) Check that air intake is clean using feather duster or compressed air, clean combustion parts as shown in product manual. If air intake is clogged with dust, then draft vent is slowed. This causes slowed venting of hot combustion by-product that will overheat combustion chamber.
Typically this condition will trip the FV system. BUT it might also trip the gas control thermostat.http://waterheatertimer.org/images/Flame-trap-inspection-325.jpg
Stand 3-legged water heaters on bricks so inspection and cleaning flame arrestor screen is ez.