I am the fellow that has the same problem as you. So I tried 2 things to prove it is not the automatic tranny.I drove my CRV away from my garage in low or 1st gear, that way there would be no shift from 1st. to 2nd. but that clunky sound was still there. Next I got my wife to stand on the street about were it usually clunks, & when it clunked I stopped & got her to try the rear hatch door to see if maybe it was locking making that clunk sound, but the rear hatch door was not locked.I am not really worried about it ,but would be nice if some-one could figure it out. I guess a person should ask every person you see that owns a 05 or 06 CRV & see if they hear that sound.