What you're describing is about what I would expect for those sizes. As Skeeter said, you can fine tune some stuff, but it'll never be perfect for long cuts.
If you are simply doing rectangles, one option could be to draw the rectangles and individual lines rather than a box. Doing this will force the cutter to start at one end of the line and go straight to the other end. This way you won't have to worry about the cuts lining up in the middle someplace. However, the lines may not all be exactly parallel but it should be close enough that you won't notice. I would also draw it so that the corners overlap a bit, like a hash mark.#