The problem isn't machines, it's people. Specifically, the guys that assemble the barrel assembly to the upper receiver are allowing the barrel to turn with the barrel nut as they're applying final torque to the nut. This results in a slight misalignment of the barrel to the receiver, but since the sights are over 2" out from the bore axis, a slight misalignment means many clicks of windage.
This problem is easily corrected if you have the tools to rebarrel an upper. Ideally, you put a piece of pointed-end drill rod in the channel of the carry handle that "points" the the front sight, and you make sure that everything lines up after you torque the barrel nut. You also need to ensure that the base portion of the barrel nut is lubed with the same moly lube you're using for the threads, but that the barrel-to-receiver interface is NOT lubed.
If you can't, or don't want to fix the problem yourself, CALL Bushmaster, ask for Jerrod, and they'll fix it for you.
-Troy