Part of "cleaning" the thermocouple is "positioning" the thermocouple. I'm sure the manual says that the tip of the thermocouple must be "immersed" (their word) in the flame, near the hot core. If the thermocouple has moved out of place, it doesn't generate enough voltage to keep the gas valve open. I have forgotten the value of the expected voltage, but I seem to recall that it is a large fraction of a volt. If you have a VOM/DVM, you an easily measure it.
Our member commodor47 put up an excellent post covering what to clean and how to clean it, complete with photos. A little SEARCHING will find it for you.
My mistake. The post I was thinking of was in regard to the refrig gas operation, not the water heater. There may be a lot of common information, but the specifics will be different.
Bill
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