This is a quote from Dyantrac who had posted this on another thread awhile back...
Granted, he was going into limp mode because he was testing this on a newer 2012 JK. I don't think that earlier models go into limp mode the same way and don't know how they will behave. I might try hitting the ESC button before you start to see if it makes a difference. If not, there is never anything normal about a bang and if it's really as bad as you say, something is gonna break on you soon.
I had regeared my 2013 to 5.13 and added a Yukon Grizzy locker in the rear. Finally after 2 weeks I found the info that the 2012+ need a selectable in the rear.
However, I had other symptoms that I no longer have after changing to the Elocker.
1. That loud clank as the OP described
2. The sometimes when waitng in a drive thru for example, I would shift to park and get a "tick" noise from th tranny.
3. I would get slipage shifting from Drive to Reverse ocassionaly.
All this had us leaning towards a tranny issue and infact it was about 2 min from going under the knife at the dealer to replace a speed sensor in the transmission when I found a thread about the auto locker/limp mode issue.
I also found that hitting the ESC button had no effect, in turns and corners i could trigger the limp mode.
I dont know what year the OP has but auto lockers seem to create havok for the 2012+ Auto transmissions.