how many marks are being scanned before it starts plotting? is the plotter merely following from the origin, or is it looking at the print an interpreting the size (segment area correction...) ...
The plotter can either measure your print and adjust accordingly, or it can cut a static plot based on a specific start point, either the origin, or possible marks on either corner of the leading edge.
From what you have described, you should be able to determine which device is off.... measure the exact size of the cuts, and measure the exact size of the prints, which one matches your original? it is entirely possible that the print you are making is the wrong size, but the plotter cuts it correctly based on an origin start (segmented area correction should help with this...)
(but media can slip at any point in both the printer and the plotter, either can give the results you see - and you may have a combination.... but no way to tell without measuring the plots and prints and comparing to the original.)