Ahhhh yes, the infamous Hunter butt slap. Rest assured that it is not some flaw in your particular boat. It's a result of the relatively flat hull shape of the hull at the stern. We too thought the boat was going to snap in half the first night we ever spent aboard. There is actually a "diaper" of sorts that you can purchase and wrap around the stern of the boat to mitigate the problem, but in my opinion they look ridiculous and would be a PITA. We minimize the noise by running about 20' of line through a spare fender (10" diameter) which we slip under the stern, cleating both end of the line on the stern cleats. We tie a knot at both ends of the fender to hold it at center. This seems to break the wave action up enough to minimize the pounding racket. Some have resorted to sleeping in the v-berth to get away from it, but that just doesn't work for me.
Good luck and fair winds!