[KB66]

I have worked with a few print/cut systems, and usually even after you put in your "cutter" marks, you will still need to find the first mark manually, set the origin there, and the RIP should tell the plotter where the other marks "should" be. (not the Mutoh Ultima, it's truely automatic) Once all marks are found where they are supposed to be, it should properly cut.

In your RIP, have your turned on the appropriate cutter marks for your model?
Does your RIP support this functionality? Have you checked with the RIP vendor for a tutorial of the Print/Cut workflow?