You may want to join the accucutquilters group at
http://groups.yahoo.com for more info. I know that some of the larger square dies require special attention to get accurate cuts (I think the 5" square die is one of them). I'm not up on the details because I don't have the large square dies, but I'm pretty sure you have to pay attention to how the grain is placed and also it's a good idea to place paper or a coffee filter on top of the fabric before running through the machine.
I use mine mainly for strips and triangles with no problems. I believe it is only the large squares that can be inaccurate without the special attention to details.