gerber system 48 plus sizing problem

hi guys can anybody help with a system 48 plus that doesn't cut the right size.
I have measured using absolute on the machine and in the X the control says 100.48 but when i measure the distance its only 97.02mm
In the Y its says 101.09 but measures 97.2
Does anybody out there know a way of calibrating it
thanks inadvance

Hi just realised how long ago you raised this question.
Hope you solved this calibration issue.
I calibrated mine through MACH 3