The size of the finished piece is what matters, not necessarily the size of the seam allowance. It's just that if you cut accurately and sew with a scant 1/4", the finished piece SHOULD be the right size. Instead of trying to measure the seam, try sewing together 3 fairly short strips that are 2.5" wide. Now measure. The center strip should measure 2" (because 1/4" was taken away on each side) and the outer two pieces should each measure 2.25", for a total of 6.5". If the measurement is less, try sewing with a slightly smaller seam allowance; if more, then increase your seam allowance. If you change your thread you may have to repeat this process to find your perfect spot for sewing.