Sorry for this trouble! As others have said, I'd take a tape measure and check the lid and the bowl to make sure that they are not out of round. The measurement doesn't really matter-- just that you get the same number as you measure the kettle in 3 or 4 spans. Also, if you have a 'true' flat surface (maybe a stone countertop?) you could set the lid (maybe the bowl too) on that to check to see if it's not quite flat.
In any case, on a brand new unit coming right out of factory packaging, if there is anything not right about it, I'd make a friendly call to Weber CS and see what they say. I've heard lots of stories of them replacing parts that were slightly damaged or out of round, and I'd expect them to make this right as well. On the whole, Weber CS is awesome, so approach them with patience and kindness and I think you'll be very pleased (and if they give you a hard time, you can always call back at another time and find someone who is more friendly).
All of my kettles were purchased used, and as others have said sometimes there is a bit of 'wiggle' between the lid and bowl (I find this to be especially true on the Performers-- I think that a round/flat bowl can get tweaked when it's bolted into the frame). And as others have said, that 'wiggle' goes away after a few cooking/smoking sessions. You'll be back to your old "clunk" in no time.