"thunk" in 2000 Mustang

After stopping heavy on my brakes and coming to a complete stop and then starting to take off, I get a "thunk" that occurs. I took my car to the brake shop and they tried to tell me it was a water bottle rolling around in my trunk(:)). So I took it to the Ford dealer and they did a total repair on the rear end axel and bearings($1700), which took care of a "scraping" noise that I was getting, but did not take care of that "thunk" when I begin to take off after stopping heavy on the brakes. I took the car back to the Ford dealer yet a couple more times and they were unable to find the source of the "thunk". Does anyone have any "good" ideas? It's definitely not the "water bottle" ( I took it out in order not to confuse any more repairmen).