I have to wonder if your rotary cutter is bad. If it is worn the blade will wobble as you cut. Maybe the little nut needs to be snugged up. Not tight just snug. Anyway what you need in seam allowance is a scant 1/4 in. 1 or 2 threads shy of 1/4 in.. This gives a better finished measurement because the thread and fabric take up space in the seam. Using a scant smaller seam will account for that difference.
Have you tried sewing diagonally across a square to make a 1/2 square triangle? Well if you mark your line exactly on the diagonal and sew on it your resulting square will be smaller then it should be. You need to sew just to the right of your line to get the exact size you want. But I don't like the word exact while piecing. If I make sure everything is exact, well then I don't have anything done. Because exact is mostly unattainable[?] for this craft. I don't know where exact is but it isn't in my sewing room. And for the most part , my quilts are fabulous. And I am positive yours are too. IMHO