It may be what is referred to as oil-canning, where the pressure changes cause the large panels of the duct to pop out or in depending on whether the pressure is going up or down.
Not a lot you can do about it. Ducts are often made with small creases (often on the diagonals) to add a little more stiffness and lower the probability of that happening. You could also try wrapping them in insulation to muffle the sound, but it may still echo through the ductwork since that won't stop it from happening.
If the ducts are not well anchored to each other, you may need some screws to hold it together better. If it is isolated to one piece, and you know where it is, you might be able to screw some stiffeners on it to prevent it from oil-canning (assuming that's what it is).
Hopefully, one of the pros may have some other ideas that may help you.