well i don't know what my dealer did but after my 15k service i never got the "clunk" again. i'm going on 18k and still no clunk.......

 

Check the luggage rack on top. I battled a simular issue for months with the Dealer until I decided to check a few things and found that the cross bars on my luggage rack was lose. Evidently wind was causing the metal-to-metal cluck that you are describing. Once again, check the hand-screw nuts on the luggage rack, you might be surprised how simple this is.

Good luck!