Actually, this is a known problem. I am curious to know if you prewashed the fabric? I think this is less of a problem if you cut unwashed fabric because of the stabilizers in the fabric as it comes from the factory. (But this is my own suspicion.)
The company recommends cutting so that the grain going underneath the roller is the lengthwise grain, not the crosswise; lengthwise grain has less stretch than crosswise. It also recommends putting a piece of paper between the die and the fabric and cutting both simultaneously. (Inexpensive coffee filters are supposed to work well for this.) Heavily starching the fabric before cutting likely helps too.
It's possible you got a bad die, but most often the problem seems to be that the fabric stretches while being rolled. Anything that stabilizes the fabric so it doesn't stretch seems to help. I know from my own use that the cutter becomes easier to turn with use, so I also think that with use the roller puts less pressure on the fabric and therefore causes less distortion as it is rolled.
You might want to join the accucutquilters group on groups.yahoo.com as this problem has been discussed many times there.