I had 4.88 nitro gears professionally installed in my dana 30 and 8.25. By the time I pulled my Jeep out of the driveway it sounded terrible and I turned around and pulled the front axle out to bring back to the gear installer. He looked them over, checked all tolerances, inspected every bearing, and said everything was fine. I didn't trust him so I proceeded to take the axle to a very well know gear guy who I trust very much. I paid him to do the setup all over again. He looked everything over like crazy, took it all apart, set them up more precisely, and they were still scary loud. We both confirmed with the jeep on the lift it was the gears in the front axle.
The gears made a rhythmic loud noise almost like they were hitting something, it sounded terrible! It was a growl like your describing. I said screw it and drove on them, they got quieter and quieter as they broke in. Nitro was a hassle to deal with and said the noise was normal and not all gears are quiet. I explained how loud they were and they didnt seem to care much. They wanted me to send the gears back for inspection to see if they met tolerances before they sent me a new set. THIS IS MY DAILY DRIVER, it would have been down for weeks. I didnt have the time, or money to do this..
The noise is still there after two years but nothing like it was before. After 1 year of hard use I pulled the cover and everything looked great, no worn parts and oil was very clean!
The gears in my 8.25 are also noisy but nothing bad. I have also heard of a few other people who have complained about Nitros 4.88 gears.