was the gear oil contaminated with any metal particles and tidbits other than the normal grey that you get?? the torque applied causing the noise to go away brings 2 items to mind. one being a u joint that is going out or a bearing in the pumpkin giving up the race. bearing, race, get it??
good place to start is to find out if there is any play in the joints or the pinion. shake the tar out the driveshaft at each joint then at the pinion yoke to see which or either have unwanted play. if the oil was clean when you checked it with very little metal dust, than i would suspect a u joint failing.