Take the lid off of the tank, and hold up the float (or ball) with your hand. Then flush the toilet. Once the tank is empty, let go of the float. I'll bet that when the water kicks on, that's when you'll hear your thud.
I once had a float mechanism that was turning on the water so quickly and so violently, that it was causing the pipe to hammer right where it came out of the drywall. The quickest and cheapest way to fix this was to just buy a different filler mechanism. And it worked.