I cant speak for the tranny being the same, but I have a 5sp auto in my 04 Accord 4cy that does the SAME exact thing. And in some cases, warm or cold, can be pretty loud. I've brought it up to my dealer, twice. The first time they said it was gear lash being taken up, and I challenged that casue the car was often moving a split second before the second "whack" was heard. The second time, all they said was, "this is normal". I hate it. It bugs me. And a fluid swap (3 qts Amsoil) did nothing.