At first I couldn’t understand what you meant, but when I tried the “Layout Chart” button in the OrgCharter sample, I also got some unexpected results.
But the Windows Forms OrgCharter application works just fine, even though all it’s all the same code.
I suspect the problem is due to drawing the links in the wrong direction, starting at the employee and going up to the supervisor. I found that I couldn’t draw (by mouse-down-and-drag) a second link coming out of a port, so I tried to start at the supervisee node. But apparently that doesn’t draw the link backwards, so the supervisee is put in a “layer” as if he were the boss.
I find if I use the “Select Two and Make Link” button to connect a supervisor and a supervisee, everything works well and the “Layout Chart” button produces good results.
If you can’t get good results by not drawing the links using “drag-and-drop”, then please describe the situation you have. In any case we’ll investigate making the ports work better–both in having the cursor showing the ports and in mouse-down at such points.