I just finished a lap size top in D9P too and ran into the same problem. I pressed all my seams the same on the original 9patches but when I cut them and turned them, some ended up with the seams going the same way and some not. I just went ahead and sewed them the way they were
pressed. It worked fine but the part that bugs me is that even though I measured the center line carefully some of the cornerstones are not lining up with the next block. Oh well, maybe the next one quilt top will be perfect. I've been saying that for the last 20 years I think.