One of the guests on one of my quilting shows said she always sews the quarter inch seam on her border piece before attaching it to the rest of the quilt. (you will sew over it again, when attaching.)
It's like stay stitching and she says it keeps her from ever having wonky borders.
I haven't tried it yet, but I've sewn clothing all my life and stay stitching is an awesome technique.
I hope it works out for you