You might need to check your 1/4 inch foot. They help but are a little deceptive. You loose a little bit in the pressing of your seams.
There are a lot of ways to check your foot and adjust your machine. Try cutting two 1.25 strips x at least 2 inches(length is up to you really). Sew them together on the long sides. Press open and measure the width. You should get something that is 2 inches x whatever your length was. If it isn't, start moving your needle to the right one "click" at a time and repeat until you get your 2 inch width. You will then always know what your "setting" is for your 1/4 inch seam.