Hi, had no idea who I was speaking to.
A couple of things to look towards...non of this is equipment I sold, so I am just going by what I have experienced as the competitor...First, I believe the FC4000 has the ability to compensate for stretch, since the cut line is bigger, maybe compensation is on when it should not be? Its probably a reg mark setting somewhere...If its not the plotter and since the HP RIP you would have gotten from that (plus I think you bought from MH) means I think you are using Onyx...I would give them a call. It could be a RIP issue.
Hope that points you in a direction that you figure something out!
Craig