I see you're using Flexi but I have no idea as to what plotter you might be using. So...
Whenever I have to contour cut questionable media, like metallic silver or gold or whatever, I always opt to use the 4 point manual option in Production Manager and, since my plotter has a built-in laser pointer, I use that and manually located the registration marks. If you do it carefully you will be every bit as accurate as the automatic marks. It saves a lot of vinyl.
Your mileage may vary depending on what equipment you're wrangling.