When you're running in 1st., 2nd., or 3rd. gear, power is being transmitted through the input shaft, cluster (counter) gear, reduction gears, and then to the output shaft. In 4th., the power goes straight in and out, and while the countergear is still turning, it's not loaded at all. It's possible the needle bearings that support the countergear on its shaft are worn, or it's more likely that you're just hearing the normal noises of power going from one gear to another. It's going to be VERY noisy in granny gear, because that one has straight-cut teeth.
Jerry