The most likely cause of your problem is not aligning the camera perpendicular to the target before shooting. Since you are having issues with this, try using two tripods, and mounting Spyder LensCal on one, and the camera on the other.
Make sure the center of the lens is at the same height as the center of the target. Now place a square, or any object with a machined right angle in it such as a book or a scrap of mat board, against the face of the main target, and look down the perpendicular edge of the object. Does it point directly towards the center of the lens, in a side-to-side direction? If not, relocate the tripod (or pivot Spyder LensCal) until it does. This type of visual offset is not uncommon, and people who cannot determine perpendicularity visually can still do so quite easily with a guide, as described here.