There could be several reasons why the shoulder seam doesn't match at the neckline.  Make sure you are matching the seam lines, not the cut edges.  A good pattern will have the back piece a little longer than the front and you will ease that seam to fit the front.  The reason is that there is a dart in the shoulder seam that has been transferred to ease.  Another reason could be that you have stretched one of the edges.  Since both pieces are cut on the bias, it is easy to stretch one or both.  If you are really having a problem, try basting the seam by hand before you sew.  It only takes a few minutes, but the result will be worth it.