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What You are probably hearing is the duct work expanding or contracting, like a cap on a bottle when You open it the pressure changes and the cap pops, the sheetmetal duct work can do this also BUT since the ducts are larger instead of just a little pop its more of a boom with a rattle sounds almost like thunder a short rumble.
I commonly seen this with new furnace installed on older ducts if You look at are larger square duct on one of its flat sides You should see an X crease to give it stability if they do not have any the noise would be fairly annoying.
Hope this helps if not please respond