stitch your blocks then press well and trim to size, you can cut them after stitching to make them nice and square. not a big deal at all really. you can sew your strips in place and make them look just right inspite of the off print.
that is a common problem with any printed panals, not just foundations. the print is put on the fabric then the fabric is wound on the bolts, and quite frequently are pulled out of shape a little. if we buy just solids/prints we do not notice it, but for pillow panals, foundations, ect the off-kilter lines show up more. you can tug it into place and press it well, should stay straight if you do that...there really is no problems after with them skewing again...your stitching will hold them in shape. a little starch will help too.