My box clunks a bit as the load goes onto and off it.
The noise that disappears when the clutch pedal is pressed is the sound of the gearbox internals rotating when the clutch is engaged. Mine does it and although I've had the car only a couple of weeks, I'd judge this to be quite normal, based on my experience of other cars. I'm certainly not concerned about mine but as suggested elsewhere, a trip to the service department and somebody listening to it wouldn't do any harm.
Peter