Hi mate, even this topic is preety old, I'm still posting here.
I got the same symptom with my E46 330d 5 speed trany and thought was differential, but suspected the gerbox as well. Under othe circumstances i changed the engine with the gearbox from another car and the noise dissapeared, and surprisingly, after 230000km the differential has no play at all. The problem is from gearbox.
This seems to come from the fact that the engine had a PowerBox installed for quite a while by the previous owner of the car, and that increased the torque of the engine to some 500Nm whereas the gearbox for this model supported 450Nn.
I took of the PowerBox and the Cars drives quite nicely at the moment.