Really a bummer when our plans are foiled.

Agreeing with celltech, loose threads will definitely "steer" a barrel off center. One easy check is to compare movement of both barrels with the barrelnut loose. With the reciever fixed measure the amount of side to side movement at the muzzle.
Obvious loose threads will be evident.

I did have one barrel with enough internal curvature that after cutting & crowning it would not zero. I indexed the curvature at 12:00 and ran the reamer in enough to re-headspace and then actually installed a scope with more internal adjustment. Just made zero but was fairly accurate and had the benefit of a 30moa rail with the windage at mechanical zero.
The Burris signature rings will most likely get you there also.
A precision nut & lug may also help if threads are loose.

Hope you find a solution.