I have this same problem when sewing over seams, especially if I happen to have a diagonal seam on the top that just couldn't go in the machine another way. When I am sewing and one of those pesky seams is approaching the foot, I lay a narrow (1/2 inch or so) strip of paper over the seam. The paper seems to stay put better than the seam allowance, and it's easy to pull off after you stitch over it.