I know in real life the AC6000 had that issue,thats why most RR went with the AC4400. I would it back to athearn,its a shame there inside of there locos dont run as good as the outside look.
Sending a blue box engine back to Athearn isn't going to accomplish much.
The majority of all the drive noise is due to sloppy tolerances. They can be made to run really nice, but it takes a lot of fiddling. I've been able to make an old grinder actually run better than an Atlas and even draw less current !
It's a divide and conquer kind of thing. Add shims to each gear in the truck to take up any slop. You want them snug, but not tight. I don't remember where I sourced them, but replacing the brass worm with a plastic one really helps.
All the drive shaft components are sloppy as well. I put a thin film of silicone on every joint and put it all together with the trucks facing straight and let it set over night. The silicone tightens up all the joints, but is still flexible enough to allow everything to turn .... and they still just pull apart if need be.
The motor itself isn't the best quality either. Cutting a few turns off the brush springs will soft the brush pressure on the armature. Speaking of the armature, I remove it and clean the commutator really well. I then flow a thin bead of epoxy between each commutator segment. When dry, I chuck it in my drill and sand / polish it smooth (old slot car racing trick). Now the brushes won't "clack" as they move from one segment to the next.
There a number of other things you can do, but that's a good start. You really can make a silk purse out of a cow's ear if you want to put the time into it.
Mark.