Something to think about. It is important that the six or eight mounting points all carry their share of the bed. If your frame is perfect and never tweaked, the combined height of cross sill, block and pad should be the same at every mounting point and they should equal the height of the rear sill mounting bracket and pads as well. Leave out a pad at two spots, and those blocks need to be taller to compensate. If the frame is bent slightly, the height of the blocks will need to be adjusted or shims added.
As for the elusive thunk, check your cross sill that is second from the front. It is not attached to the frame but hangs very close to the frame on some trucks. It can contact the frame when you hit a bump.
Mar-Ktech