How many marks are you using? For optimum accuracy, use 4 if you can with your particular setup.
How large are the prints you're contour cutting? The smaller the area inside the registration marks the more accurate the cut.
Vinyl running straight in your plotter most likely is not your problem. If you're locating the marks manually, you're off a bit. Very common. If you're letting the hardware locate the marks in one way or another [there's at least three ways to do this] then you might want to calibrate the plotter's auto sensing tackle.
All of the above is presuming that your equipment, both printer and plotter is consistently linear. Meaning that some arbitrary X or Y distance remains constant over the entire job. It would be extremely rare if this were not the case.