I just did one the other day, and was having the same problem, although I don't recall having that much of a problem in the past! (Every quilt has it's own quirks) So I did the marking on the long horizontal strip, as Kitsie showed us above. Then when I was sewing, I switched the stitch length to baste when I came to that section. After checking to see if it all lined up, I went back and stitched the basted areas. If it didn't, well, it was easy to remove the basting stitches to realign.