I think that v5.70 addresses that issue but not quite I believe. I'm attaching some files with export and pictures. We don't do full sheet flips and it's still doing some of the flip operations as face operations. It's happening with our 306 tool. Anyways check it may be the issue was solved in v5.70. Let me know if you need more information
I've encountered the same problem with single part flip ops. When the flip operation part was nested by itself, say a sheet of the same flip op part, it worked fine; but when nested with other parts a dado was produced on the wrong side. I can't post any files at the moment, but I'm using the latest updates. My work-around was to nest the flip parts separately.
My problem occurs on the same tool that is easy to isolate so my operator decided to skip it whenever the machine picks it up and move on to the next tool.