Gary, You need to isloate the duct from the floor. It would seem that the duct must be strapped directly to your floor joists , or worse, to the subfloor. Ideally, you need to "hang" the main duct so that it is not up against any of your wood structure. You may need to have a sheet metal guy provide you with a deeper boot which comes down from the heating unit (assuming it is a down draft unit, which it sounds like it is).
Then, you can lengthen the hangers and get the fool duct away from your structure so it doesn't drum.
Any other method, such as trying to stuff some insulation between the structure and the duct will probably still result in drumming, but you could try it.