Clunk in transmission when you stop 04 Dakota 4x4 Auto

Maintenance/Repairs
1

When I make a hard stop from about 35mph, right before the speed of the car gets down to zero, there is a loud clunk from somewhere close to the automatic transmission. Sometimes it is a double clunk. The dealer initially said the computer required an updated program but them but when they found out it had the updated program they then said it was the nature of the beast. HELP