The clunk comes from the stickyness of the clutch. When the tranny is in neutral the clutch is not moving with the engine, it is held stationary to the output (clutch back) part of the drivetrain... even when you pull in the clutch lever, the plates are still in contact and because of the oil, the plates stick together and have a good ammount of suction friction between them. This circumstance stays until you shift into gear and the clutch starts slipping, which quickly lubes everything up better and lowers the clutch friction. The clunk comes from the shock of the clutch and clutch housing being more or less instantly accelerated to the speed of the transmission output shaft as the gear is engaged.
I should add, every wet clutch on a bike I've used has done this.