I always use a scant 1/4" seam -- but if you haven't you should measure from your needle to the mark you are using for 1/4" (or the edge of the foot). 2 of my 3 machines need to have the needle moved to the right to get an accurate 1/4" seam.
I was at a quilting class about a month ago and we had someone who was consistently off. Come to find out she was was not consistenly cutting on the same side of the ruler line for each piece.