If you go on the 'Quilt in a Day' website, they show how to properly use the ruler. As was suggested earlier, put the dotted line (seam line marker) right on top of your stitching line. This allows for the thread loss when you press the piece open. One other thing that can make the piece a thread smaller is the thread you are using. This is why, by placing the ruler sitting on your stitching line, you should come out with a block that is the correct size.
Charlie