Spot color replacement doesnt make a difference. Now that you get the cut into onyx... I'm not sure why it's cutting wrong.
I just E-mailed you a file. It's just a 1" x 1" square, on a 2" artboard as .svg. Open up Onyx cut server, click open, and load that file - Then send it to cut. It should just cut without needing any marks or anything. See if it cuts as 1" x 1", or if its bigger. Then you should be able to eliminate the ripping.
I use a Graphtec, so I'm not much help on the cutter side. Onyx does look like it's setup right, which leads me to believe it's a cutter issue. But just to rule it out... load the file and see what it does.
Also...On our version of cutserver there is a ruler with how big the sheet/roll is. I'd double check that to make sure it's right. Theres an option to change magnification in the cut server also. IT may just be a graphtec setting, but I doubt it.