If you're hearing it actually step, then the problem is likely in the artwork. Open the artwork in a vector design software and show the nodes. If your lines are covered in nodes, it's the artwork, not the plotter.
Also, the CE 5000 is an old entry level plotter. If you're cutting heavy sandblast stencil, it won't hold up to that kind of use for long. Check the carriage and see if it wiggles on the rail. The spring bracket that holds the bearings tight may have gotten bent. It can be bent back into a slight crown that will force the bearings down further.
Good Luck