One possibility not mentioned is that the stove may be running too hot in a confined space. Alcohol stoves work on burning the vapor. If you heat the alcohol you get more vapor. If you heat it too much, you boil the alcohol and can get run away in which you burn off your fuel too fast and never get a boil with your water. The Trangia is known as a 'stormcooker' because the higher the windspeed, the faster the stove cooks. It has been finely engineered, however, to prevent run away, by decoupling the stove from the support and the pot.
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If I wouldn't eat it at home, why would I want to eat it on the trail?