Whack the seat stays the direction you need them to go, at the bridge. It's not uncommon for the seat stays to be a small amount out of alignment with the dropouts in near perfect alignment. The depth of 1 thread is enough of a difference at the axle to make a significant difference at the seat stays, so the dropouts could look and measure aligned. Actually before hammering on the seat stays, measure, measure, measure to see how far out of alignment they are at the bridge. I'd make sure the seatpost and head tube are in alignment, stick the bare frame on a few 2x4s to keep it off the ground and have a whack with a deadblow hammer right at the seatstay bridge. Then measure everything. You could keep an axle clamped in your dropouts to ensure you don't put those out of alignment and create another confounding factor.