My truck is a 2011 SuperCab 4x4 with the 5.0, 3.55 gears, and currently around 91,000 miles. Mechanically the truck has been rock solid since I bought it with 67k miles. I use it mostly to commute to work and as a run around vehicle, but its also pulls my 29 foot travel trailer a handful of times per year. Usually these trips are local or no more then 3-4 hours away. This past summer its started developing a strange clunking sounds coming from what sounds like the rear of the truck when starting or stopping. The first time it did it was when I got back from a work trip to St Louis, about 6 hours from me. I panicked a little, but then it went away after a few days. It's come back and went away several times since then, always after I take a work trip. The last time was this week when I drove to Atlanta and back. It started when I got down there, I filled the gas tank up, and it went away...strange. Then it started again when I got back. Now its gone away again. It almost feels like the transmission gears are still spinning when I stop because it'll clunk twice. Starting is just a straight up clunk. Strangely, when I towed the RV in November 90 miles away it didn't do it at all. My towing speeds are usually somewhere between 60-70 depending on traffic, terrain and road type. Driving unloaded my speeds are somewhere between 70-80 depending on speed limits. Any ideas what this may be?

 

I'd check rear suspension for something loose, starting with the rear shocks. Since putting a load on it seems to fix it, it would seem that something is a bit loose until weight is applied.

 

I went through that same thing with my 2011.