So I have been battling trying to figure how to keep this from happening. Please look over my two photos that I have attached. These were both from a very short runs and they both were off in the X direction. The Y direction looks dead on and is not a concern. Here is my equipment stats Onyx 10.1 rip, HP LP25500 Latex printer, FC8000-60 cutter ( Settings for this job are Condition: 3 Slot three .75+/- Mark size. I have tried doing Mark Scans as well Sensor readings and adjustments, but having been successful of ridding of this problem. Any pointers? I have also double check artwork and die line to make sure they were not skewed prior to printing.
I don't know the REAL fix with your system and plotter, I do know HOW I would fix the issue so I could complete the job (work-around).
Use a loupe (magnifying glass) with a scale built-in (see below) or a regular loupe over a engineering scale (has many small graduations), and measure how far off the cut line is off.
Then open the art file and move the cut line the same amount as you measured, in other words, move (offset) the cut line towards the front the exact distance it's off in the photos you showed.
Then when you go to cut the cut lines, you will fool the plotter into cutting the lines in a PERFECT distance from both the front and back.
Again, you must precisely measure how much the cut line is off, then make a correction, moving only the cut line in the artwork the measured distance towards the front, leave the artwork and registration marks as they were (don't move them).