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Hello, it is likely that you are correct, the efficient furnaces need W1 and W2 terminals on zone controller, that is first and second stage heating... if your zone controller only has W or W1 on the terminal strip that has wires running to the furnace, it may have been wired to run on stage 2 heat all of them, when only stage 1 heat was required.
That should not fry the zone controller though... nor cause any damage to the furnace.
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