If auto calibration is off, you can manually adjust the print to cut alignment to fit your machine. Do the following:
Do a blade calibration, pick the best number and letter as you have done and do a test cut. Do not remove the mat or hit accept or repeat. Look at the cut inside the test image. If it needs to be moved to the right, pick the number at the top of the page with the cut to the right of the print line.
If the cut line needs to be moved down in the test image, pick a letter where the cut line is lower than the printed line (if your off significantly, you will have to pick a cut line that is 2 or 3 numbers or letters away from the best aligned print and cut line).
Hit Test Cut again and you will see the new position of the cut line in the square spiral. If you're happy hit Accept, if not, keep repeating the process until the alignment is acceptable. If your spiral cut is getting too many cuts in it such that you can't tell where the new cut is, then hit accept and repeat the process above.