Wait up... for me Kiss cut and CutContour are the same thing. My CutContour layer is my kiss cut layer.
Yeah, I think that might be why your way works. ;p
99% of what I do is just a single through cut of all my stickers, and I use the CutContour prefix for my setup in Illustrator and the RIP. So when I wanted to do a sheet that had kiss cuts on it, it seemed obvious to me to use the default Kiss prefix for the peel-out "top" little elements, and keep using CutContour to do the final "die-cut." Problem was, CutContour always wanted to cut first. Way around that was eventually just to create two new custom prefixes that had no relation to any of the default choice. Like (ABC) and (XYZ).
Boudica: Going back over things, I AM going to try your reordering thing in Cut Server. The reason I don't have the option is because I have my Cut Server to Automatically Cut Files to a folder, so they are never in Cut Server for more than a split second. If I uncheck auto-cut I think they'll hang out in the queue and I can pop open their individual settings and do what you described in your first post—reordering the cut layers.
A lot of the issues I think we're all having is just because we use different definitions to do the same thing, but I appreciate all the help thinking about things.