If I understand you correctly the two pickups are wired differently. This could be just different batches, or it could be an error. As you sound experienced with electronics you could probably do a bench test to check this given a decent meter, but I'm not the best person to give the details. It's principally polarity that might be an issue. You can probably find instructions on the Web to check humbucker polarity, or will someone who's done it comment.