Hmmm... This is interesting. If you raise the box top slightly, it doesn't make a difference. If you raise it the radius of the tool or more, it works correctly. You can then drop it back where it was originally and it will work correctly. I tested with a Ø12mm ballnose, so I raised the box top 6mm. It worked correctly. I then moved it -6mm and it still worked right. This isn't a solution, only a workaround. There does seem to be something not quite right here. I will ask Joakim to test this himself (with your file).
Thanks,
Dan
(Note: The opinions expressed in this post are my own and are not necessarily those of CNCzone and its management)