Mine has the same clunk and it's only at lower speeds (below 15 mph) or while coming to a stop. I never hear it while accelerating or driving at a steady speed. Hopefully when I drop it off Thursday, they'll figure it out; and this time I'll request going on a test drive with a tech before I leave the car. Last time I had it in, I insisted it was the motor mounts and they said they checked and the mounts were fine. The more and more I hear it, the more I think it's suspension related.
I'll keep you all posted.