Does it happen on changing down to third? Any crunch? If it was a third gear synchro issue down changes would be worse. DMFs can rattle when the clutch is pressed but this should happen across all changes and when idling in neutral. My noise occurs in gear. If it appears during the change with the clutch still on the floor resonance can also be ruled out. Might be worth checking the oil level in the box during the next service (filler plug is at the from of the box, accessed from below with an alan key) just in case the third gear set is at the top of the box. Other than that I'm at a loss. I've heard very little about box issues in the x so I guess it's a case of drive it and see. May also be worth using a 'screw drive stetescope' on the top of the box with an assistant engaging 3rd (but obviously keeping the pedal on the floor, handbrake on and wheels chocked) to see if you hear anything. I'd also advise doing the same with the bellhousing, in neutral, to see if the DMF is rattling. You can also sometimes exagerate the DMF rattle by facing up a steep hill, engaging first and slipping the clutch a little (only for a second or two).
Regards,
Dave