If I understand, you are getting getting good groups, but a changing POI. With no other variable changed, it does suggest a magazine related issue. But, there might not be anything wrong with the mags, because in some rifles (don't know what rifle this is) the insertion of the magazine can slightly alter the barrel alignment it everything is not properly secured. One MOA, or a half-inch at 50 yards can be the result of a shift of only .001". Usually, if a magazine alignment problem is causing significantly damaged pellets, the accuracy will be poor, with wide flyers, at least that has been my experience. If the magazine alignment is not off much, but yet not perfect (very common), then accuracy will not be as good as when loaded single shot, but not terrible either.