Most of the time we square up our mats on the Fletcher 3000. We had some trouble with the mats being slightly off prior to this. The method I have found works great.
Place the mat in the cutter and leave at least 1/8 excess and make the cut, turn the mat clockwise and make the second cut to size, for the final cut, turn the mat clockwise and cut to size. This way you have 3 sides that are squared. After we started using this method our mats are all true to size and always line up. Of course the Wizard can cut the outside, but depending on the size of the mat, it might not be an option.