Could be a couple of things. First of all, make sure you are always using the same line, ie: are you a hair over the line or a hair under the line....... 2nd, you might be cutting too many layers at once or not pushing down firmly enough on the ruler when you slice thru. (Be careful, 5 stitches tell my story!) 3rd, use a ruler than extends over the top and bottom of the fabric you're cutting.
Anyone else have any suggestions, these are the things I would look at.