The cutting edges are positioned that way to make rolling fabric through the machine easier (and to minimize fabric stretching). You need to line up fabric with the cutting edges of the die, not the outside edges.
The 5" square is the die that has the most problems. Be sure to measure your squares to make sure they actually come out square. If not, you may need to use a paper filter between the die and fabric to avoid stretching the fabric as it goes through. There are other tips for using the dies too, I think. You might want to join the accucutquilters group on Yahoo for tips, ideas, etc.