My Whirlpool Hot Water Heater, turned 3 years old in October of 2012, does something that is fasinating and yet annoying. After a long burn, ie: someone takes a shower, the pilot light no longer engulfs the thermacouple. Therefore, about 15 seconds after the burner turns off, the pilot does as well. You can relight the pilot immediately after this but the flames still does not engulf the thermacouple so it will not stay on. If you wait 1-2 minutes after the pilot tunrs off to relight it, it works... until the next time the burner kicks on. I have tried letting the burner burn for a few minutes and then turn the temp down until it shuts off and the pilot stays on... it is only after the long burns that the piot flame gets mal-adjusted. Anyone have any thoughts on this?

You need to either clean the jet or adjust the pressure for the flame. There is an adjustment screw on the gas valve. Alternately, you need to check the gas pressure.