I think you have the X and Y axes confused. To the plotter the Y axis is the direction of carriage travel and the X axis is the direction of media feed. The X and Y axes of whatever it is you're cutting might not map into the plotter's if you have rotated the cut at some point in the process.
I'm not sure what you're doing but if you send the job to the plotter such that the X and Y axes of the job match the X and Y axes of the plotter it should work the way you'd expect.
Not sure about Cutting Master but Flexi will, generally, cut the first column along Y then advance the media and cut the next. And so on until the media is fully advanced. This obviously minimizes media motion which is the optimum way to cut.
Not according to Cutting Master. The X copies run the direction of the cutting head travel. The Y copies run the direction of the media travel. The whole point is I do not want the media advancing along the Y column first. I want the copies along the X row cut first and then advance the media along the Y column to the next X row etc. I can't believe anyone would the whole Y column (could 20' or more) advanced and then retreated to the start to do the next Y column.
Like I mentioned before, if no registration marks are used then the cutter does the X row first and then advances the media to the next X row etc. I will have to see if there is a way I can make Flexi do this with registration marks created in Illustrator with Cutting Master as I can't use Flexi to print with.
Again here is Graphtec's tech response.
"I did double check and confirmed with my programmer liaison on the cutting priority in Cutting Master with regards to the multiple registration marks.
I certainly understand the issue in media movement and I apologize for any inconvenience.
I will definitely bring this issue up for improvement of our Cutting Master."