I've had this happen. I think the batting causes my creeping problem. What happens for me is that when I baste the quilt, it takes a tiny bit more fabric to go over the curve of the "puffiness," or I guess loft, of the batting. When I then quilt it more closely, the fabric has to lay flatter which causes a wrinkle. And it's this "wrinkle" that works it way out to the border and can result with the top and bottom not lining up as planned. When I switched to a thin cotton bat, my problem disappeared.