My water heater pilot goes out immediately after the main burner shuts off. New thermocoupler and cleaning did not help.

A plumber replaced the thermocoupler and cleaned the inside and replaced the piezo-electric starter. No improvement. Sometimes it will go for days without going out, then it will not stay on. I have noticed that when the main burner shuts off, the pilot will go out with it. There are no leaks and there are no restrictions to the flue. (Checked on the roof). Will a new gas control valve assy fix it? The parts are still in warranty.