Are you pressing the seams in different directions. Pressing the seams on one piece one way, pressing the seams the opposite direction on the other piece helps them 'nest'. They will match everytime as long as the pieces have been cut correctly and the seams sewn consistantly. Don't over 'press' your seams.
If seams/pieces are 'ironed' the pieces will sometimes become
misshapen causing the seams not to match as well.