I just graphed it. The 3 1/2 square matches the (2" x 6 1/2" sewn together), but if you sew 1/4 either side of a drawn diagonal line, the 6" piece and the 3 1/2 inch piece will not match.
If you haven't already cut all the 3 1/2" *squares*, you can cut them 3 1/2 by 3 3/4. Then the sewing line on the long side piece side of the diagonal drawn line goes all the way to the edge of the 6 1/2 piece.
What a pain! So sorry for your troubles.