I have had the same problem with my Graphtec FC-7000. Plus, when it would read the calibration marks the cut would be off, even after several recalibrations. Someone here on this forum posted the solution that I have been using for about a year now. It takes maybe 2 minutes longer, but it works EVERY time, perfectly. I'll try to explain it. When you are ready to send the file for contour cutting, enter the Rip & Print window, click on the Advanced tab and click the Contour button. Select "4 point" from the menu of registraton mark types. It is usually the first one on the list. This will print a bombsight at each corner of your print. When you click to send the contour cutting job to the plotter, it will ask you if you want to use "interactive" or "digitize." Choose "digitize". Next, it will ask you if you want to use the light pointer. Select, "Yes." The red light will come on. With the plotter's arrow keys move the media and the carriage until the light points dead center of the 1st registration mark. When you have the light centered, use the mouse or press enter. The software will move to where it thinks mark #2 is, but it probably will not be in the dead center of the mark. So, again use the plotters arrow keys to move the light until it is in the dead center of mark #2. Press enter again. Repeat these steps for mark #3 and mark #4. After all 4 are centered, the software will tell you to replace the light pointer or something like that. Just select whatever means "Continue" on your monitor. You do not physically have to change anything. The plotter will use whatever condition you have selected. Then, the plotter cuts your contour job. Works every time for me. Hope it helps someone else out there.
