Which version are you using. Download the current one (
www.craftedge.com) and see if that makes a difference. I would recalibrate if you are using an older version as you shouldn't be "that far" off.
There are instructions in the Learning Center for fine tuning the calibration so you get it spot on, but again, you should be pretty close if the calibration is done well (not passing judgement) and then the laser is well lined up when registering the marks. I keep a little clip light on the end of my cutter to be sure I am dead center when I register the marks. Once I register the first mark, the next two come very close and need little adjustment. The current version on the site is 3.057. Check your version number. I am testing a newer version right now.... but I am pretty sure (someone confirm this for me) that the version on the site corrected the timing out with the registration.
Keep us posted...