Mine is definately RPM/lugging related. I have a 1 piece driveshaft and the truck did it with the original trans, NEW replacement trans, new TC, shift kit, etc. I have had 5 different iterations of the transmission in the truck and it has remained consistant.
Sam, I'd probably have been escorted out of the dealership by now if I were you. Did you check the tightness of the splines on the tailshaft of the trans (or T-case) and also on the slip joint? I had that cause a shudder in a car once.
Another thought: you might try hooking up a video camera to look at different parts of the driveline to see if that helps.