Are you using the AR30 rail with the integral recoil lug?
It is easy to determine if set up in the right equipment, harder to say otherwise. You may be able to actually see if the scope is not locked in parallel with the barrel, but that does not gurantee the bore is concentric with the OD or even straight at the muzzle. A Leupold boresighter or the like may help in this, but you still will not know if the barrel/receiver is threaded off axis or the base holes.
I don't know how Armalite indicates the barrel in before chambering and threading but, if they setup with a tapered rod at the breech with two indicators on it and let the bore at the muzzle end run wild and failed to index any RO at the muzzle to to 12 O'clock, it can be pointing off to one side.
I would take it to a gunsmith and let him determine the cause, shouldn't take long at all. If it weren't for the crosslug in the base, and I'm not sure how tight it mates to the receiver, I'd think it was the base screw holes off. That recoil lug may fit tight enough it doesn't allow it to though??