I honestly think the problem hear is operator errors, no offence meant but do you understand the difference between a vector and Bitmap images, if your cutter as you say appears to be looking for registration marks that's because it's being told there is a print on the vinyl with registration marks and usually this would have a contour line around it which is cut leaving one with a sticker.
vectors are mathematical if you stretch a vector it gets bigger with no distortion but a bitmap will pixellate, plotters only cut vectors, you need to learn more I think it's difficult through this medium if you could find someone to sit down with you and the machine even at a price I think it would be worth it if it gets your business up and running.