The company is aware of the problem and has specific recommendations; try calling them. Also, people on the accucutquilters group at
http://groups.yahoo.com are very helpful.
Up to 1/2" of lopsidedness is a *lot*. Are you by any chance using prewashed fabric that has not been starched? That would be more likely to stretch than unwashed fabric. In either case, starching the fabric first will help prevent stretching while going through the machine.
Placing paper on top of the fabric is the tip that I have seen most often. You can use coffee filters for the paper. It does need to go on every time you run the die package through the machine.
Also, an alternative for some sizes is to use the strip cutting die to make squares (rather than a square cutting die). Basically you cut the strips first, then place the strips perpendicular to the die and run through again to create squares.