If you only get the clunk WHILE shifting, with a heavy load on the gears (I.E. pedaling hard, especially uphill), it's probably normal. My understanding is that hub gears are kind of like a manual transmission... when you shift, you're bringing different internal gear sets into play. So, like a manual transmission, it'll shift a lot easier without a load on it. In a car, you use the clutch; on a bike, just stop pressing so hard on the pedals for a moment while you shift.

With no load, it's easy for the gears to move slightly to line up as it changes from one set to the next. With a load, the clunk is probably the gears finally lining up and the pressure on the pedals forcing the shift to be harder than normal.

Now, I'd still check the cable, that never hurts. On my wife's bike with a 7-speed nexus, you flip the bike upside down, put it in 4th gear (I think), and there are two red lines, one on the outside of the hub, one on the moveable thingy that the shifter cable attaches to (at the hub end), and they are supposed to line up. If they don't, adjust the cable until they do.