Are you sewing a 'scant' 1/4" seam allowance? I had the same problem you did until I learned that the space the thread took was taking up some of the space the fabric needs when it folds over. Try to sew your seam just a teeny bit to the outside of your drawn line and see if that helps.
Or... you can use this method on Bev's Quilting page which doesn't require any special rulers:
http://tinyurl.com/6qp3y5a
Easy peasy! Good luck!
