I always load quilts with a seam parallel to the rollers, never the way you loaded it. If the back has many seams, I load it with the most seams or the longest seam parallel to the rollers. I agree with everyone else that your simplest and best solution is to reload it the other way and be done with it. Did you also remember to sew the backing seam with half inch seam allowances and to press them open? Makes for less bulk that way.