Good that you bring this up, i've come across quite a few reports of trouble with the third gear, even in some cases it breaking and causing massive damage. The french Motomagazine reported just such a problem during their 50000 km test of a XTX. It has been suggested this could be caused by shifting into 3rd at too low speed and then throttling up hard. I hope the clack noise isn't related to this, but could it be a warning sign ? Not likely in my case anyway, since I'm old and rather slow.