My tj used to make a loud thunking because my gas tank skid plate didnt have the straps over the top so my gas tank would bounce everytime i hit a bump. Its probably not likely thats what you hear, but it is a possibility.
Turns out, the violent thunking was cause by the aussie locker not handling the 33s. Replaced with spider gears and left the locker in the front. Runs like a dream now and the driveability in comparison is unreal.