Years ago a group of us made "noel" tablerunner, except I used a different design instead of the words and not Xmas colours. We all had this same problem. I "fixed" mine by ironing carefully all the little squares, then stitching close to the edges whether they had lifted or not, and then doing a fancy stitch in black to make sure they stayed in place. I'll try to post a picture of a close up so it might help explain it.