Don't know anything about the heater bypasses so this is just a thought. When the pump is running you have water being 'pushed' thru the heater. When the pump is killed, you now have the mass of water in the pipe after the pump trying to keep moving and now the situation has changed to one of 'pulling' water thru the heater, possibly a valve in the heater or something else in the heater is slamming shut?
Al
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