Hi Wojtek,
What type of analysis are you running? Where does the message appear? (In a pop-up? In one of the log files? Which one?).
I am not familiar with the message, so I don't know what the cause is. Out of curiousity, have you tried defining a local coordinate system? (Right-click on "Coordinate Systems" in the browser > "New...".) What happens then?
If the problem still persists, you could provide an archive of the model, and maybe someone could test it. That would demonstrate whether the problem is in the model or something unigue to your system. See "Create, Post, or Provide an Archive of your model".
