No zoning, three air handlers-- then most all the above...never mind
But you could still have a timer in your home for ventilation which cycle the fan(s). Or, in your thermostat you could have a ventalitaion/circulation cycle and the clunk you hear after the air handle shuts off is "tin canning" from your duct work. But that should me more then obvious to anyone in our field, I would hope.
Tin canning comes from the duct expanding and contracting when the air handler blower starts and stops which pressurizes the duct work.
My bet right now with this new information is "tin canning."