I agree that dealer should take care of it; but no harm in you investigating for the cause. Two mechanical flaws that will yield strong felt/heard "clunk-clunk" in suspension are the fairly common very loose front fork bearing pre-load and far less common very loose rear shock absorber mounting hardware. Even more rare, but not unheard of, damaged swing arm bearings or seals (when my bike was delivered to me, the swing arm bearings on the right side were damaged and binding - not loose, but loose is possible). There are a multitude of minor clunk-clunks that can range from loose lugs to improperly installed Tupperware.
To check front steering bearings for excessive looseness; place bike on center stand, place a prop under the front of the engine to hold front tire off of ground, grasp handle bars and vigerously pull up and push down in alternate fashion to see if the clunk is heard. If not, slow side to side motion can verify if bearings are notched (they should feel completely smooth stop to stop - no roughness or "catching"). Unless you are a decent home mechanic, checking the rear shock and swing arm are gonna be up to the dealer. Other loose stuff just needs to be eliminated or confirmed by checking everything out.
prs
Hard to know exactly what you are describing, could be a weak spring on the center stand or side stand? 
