Tony,
I do hope for you that it is just the thermocouple.
I don’t have a high degree of confidence in this product.
Initial introduction of this product was marred buy a class action lawsuit…
http://www.consumeraffairs.com/news04/2008/05/whirlpool_settlement.html
And while you have the “New & Improved” version don’t even think the problem is fixed.
If you look at this link http://www.consumeraffairs.com/homeowners/whirlpool_water_heaters.html
You will notice about 179 pages of customer complaints on the Whirlpool Water heaters.

This isn’t even the whole picture!
The Whirlpool Flame Guard & Flame Lock water heaters are made by American Water Heaters, a subsidiary of A.O. Smith. Whirlpool is not the only brand name they make with this design.
There are a bunch of other brand names made by this company and the design is the same on all the brands. This makes avoiding the defective ones difficult indeed even for the educated consumer.

IMHO the problem is a poor design of the air inlet. The problems started a few years back when FVIR (Flammable Vapor Ignition Resistant) designs were introduced. FVIR is a safety design. Lets say you had a water heater in a garage and you spilled gasoline while filling the lawnmower. If the gasoline vapors reached the combustion chamber of the water heater the pilot light or burner if it was on could ignite the vapors and the flame could travel back to the puddle and cause a fire. So this is a good safety idea. However, it involves sealing the combustion chamber of the water heater and placing some sort of flame arresting device across the air inlet that allows air to enter and the flame cannot exit. When a higher than normal flame is detected the water heater will shut down.

The problem is that these devices can be somewhat restrictive in terms of air flow and more so when they get clogged with things like dryer lint and dust. American Water Heaters has placed the air inlet on the bottom of the water heater and the opening is relatively small. Further more think about where water heaters are usually placed and how many of them are in areas where there is a dusty environment, laundry areas, closets, basements, & garages are all typical locations. A small opening and placing it on the bottom has made this a dust magnet. Once the air inlet is clogged the flame starved for oxygen gets yellow and goes higher tripping the unit into shutting down.

I’m afraid that it will not be as simple as replacing the thermocouple that Hashish is sending you. cleaning the air inlet is another part of the equation and so is keeping it clean. Other parts have also been problematic like the gas valve. The skinny is as long as you have this water heater it will be a roll of the dice as to whether or not you have hot water. As a Plumbing Pro I don’t like working on these units as they are a callback waiting to happen, and I prefer not to become involved with products that have a design flaw that may have a customer complain about “my repair” not being a good one. If you plug in other brand names other than the American Water Heaters brands you will see that no other company has as high a number of complaints. They do indeed have a problem and I also wonder how much of a liability they have set themselves up for when they send parts to customers like thermocouples, gas valves and burner assemblies expecting to have the customer install these parts themselves. Personally I’d expect this level of repair to be done by a Plumbing Pro. Gas repairs are not to be taken lightly. Nasty things can happen like explosions, and carbon monoxide poisoning without any warning.

If you seek to replace this water heater I would recommend Bradford White water heaters. IMHO they have probably the best FVIR design on the market today.
http://www.bradfordwhite.com/fvirtech.asp
Here is a link where you can find a Plumbing Pro that installs Bradford White water heaters.
http://www.bradfordwhite.com/finda.asp
Bradford White water heaters are only sold to licensed plumbers.

Any updates for us?

Did you ever find a solution to the problem, I was wondering,

Joseph