Funny that your contour cuts are also off that same amount then. Are you using registration marks (read by your plotter) to make your cuts?
I have the same problem, and have checked my media comp over and over, the only thing I can figure is the heating and cooling process is somehow making my print stretch before print, and it becomes shorter once it cools. (shrinkage!) I dont use the same rip as you, so can't address it via software, but check your media comp. Hope this helps some.
Nonsense. The registration marks are heated and cooled right along with the rest of the print.
If a contour cut is off it's most likely something other than printer size compensation and/or the media changing shape.
Understand just how the registration marks work and you'll understand why the problem is somewhere else. Here's how it works...
When you create the job in Flexi the software locates the registration marks in an exact rectangle surrounding the actual print. The four corners of this rectangle are known to the software. When the job is printed along with the registration marks these marks not longer describe an exact rectangle. This is because of various mechanical tolerances, temperature, whatever, in the machinery doing the printing.
When you load the print into the plotter the marks are read and their current physical location now describes a space that may or may not be a perfect rectangle. As long as these points are known it is a matter of some simple arithmetic to map any point in the original perfect rectangle in the design to whatever the actual space defined by the marks on the print might be.
When you use the automatic marks and sensing this is most likely done in the software. When you use manual marks unknown to the software, this is done in the plotter. It really doesn't matter where the mapping is done, only that it is done.
This is why you can load a print into the plotter skewed and it will still contour cut accurately.
The only assumption made in this process is that any distortion will be linear and, other than some horrible hardware or software malfeasance, it will be.
Thus it should be obvious that no matter how the print is distorted, be it feed compensation, temperature, or divine intervention, the plotter will accurately map every point from the original design onto the physical space defined by the actual registration marks.
One thing to notice is just how is contour cut off. Is is correct close to the first mark (lower right) and does it get worse the closer to the fourth mark (upper left)? Or is the error the same anywhere on the contour cut?
If the latter the you need to adjust your plotter's sensor to blade distance. If the former then you probably have some sort of media feed problem in your plotter.
I can't help with your issue. I thought this thread was about something totally different when I read the title... my bad! 
