What you describecould be caued by a few things, but not the thermocouple. I would bet your problem is caused by one of the following:
-Gas pressure too high.
-Flue vent plugged up
-Combustion chamber is plugged up and sooted.
-Pilot flam is too low
If the gas pressure is too high the gas would rush past the pilot flame and fill the chambers and then once its filled the gas would come down to the pilot and a condition called delayed combustion can happen. This would be a small explosion and the flames roll out of the chambers looking for oxygen to burn with. The same result can happen with the combustion chambers being plugged up, the gas fills the chambers and there is not enough draft and the flames roll out looking for oxygen. This is usually indicated by the flames continuing to burn out side the chambers. If the pilot flame is too low then the delayed ignition can occur. I'd be willing to bet that its gas pressure related because you say you replace the thermocouple every year.