When you're ditch-stitching on a seam line in which the seam allowances have been pressed alternating directions, you have to make a little diagonal stitch when you move from patch to patch. So just do the same thing when you get to a corner that isn't perfect. Which is perhaps what cjsews was suggesting. I had to do that on a recent quilt in which not all corners were perfectly matched (hmm) and it really isn't noticeable in normal use.