Flexi contour cut issue

[os101king]

Ok, I'm running a Mutoh 1204 VJ and a Graphtec FC7000 MKII 130. Just recently my contour cuts started acting up. First I noticed on a 12' run, about 14-16" of the cut was off by about a half inch. The rest was close. Next problem that appeared was a tendency to cut a full inch off on repeated jobs. Next issue was reading the registration marks in a different order than it should have, then shooting the vinyl out of the plotter as it looks for a final mark that would have to be 4' past where the vinyl stopped. It cuts fine on color vinyl, no issues. I recently updated to Flexi Pro 10.5.1 and Production Manager of the same version but have been doing fine with that until now. I tried running jobs that had previously cut correctly to no avail, however I had cleared out my old jobs in PM so I don't have them saved, I had to re-process them. Is there any chance this could be software? The sensor will scan the first mark then the second and then just fire the panel out of the rollers. It keeps doing the same thing over and over. I bought it from GRS... I love those guys and they've helped me in the past but I can't get anybody to call now that everyone's switching to service contracts!!!!!! Anyone have any idea???

For clarification, I'm running a PC with Windows 7 Pro.