Back to the OP's question and observation that the popping goes away when the water heater is off....
I've heard popping from the water heater, but not sure if it's minerals popping off of the heater rod, water getting hot enough to form a bubble under a mineral deposit, or just the water heating up. Have you checked the sacrificial rod lately? Sorry I don't know if the Aquahot has one, but most water heaters do.. maybe flushing water heater tank might reveal something.
Last time I winterized, I was amazed at the amount of mineral slivers that came out.
Just a thought...
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