Comment 3 for bug 716145

Although this discussion is a bit old, let me add the following:

I confess I do not understand the comments in #2. As I understand Inkscape design, the start and end points of connectors are in the centers of the objects connected, but the part of their path covered by these objects is invisible. This can also be seen in the examples of http://tavmjong.free.fr/INKSCAPE/MANUAL/html/Connectors.html.
Thus, I do not understand the comment in #2:

> There is no part of those lines that is 'below' or 'hidden' by the opaque object the connector is attached to.

Now supposing that Inkspace should do would I described and what the help file displays, my problem is the following:
In a given diagram, some of the connectors that I draw behave as desired, while others overlap their connected object. I have inspected the SVG code; but with my limited understanding of SVG, I cannot discover the relevant difference between the specifications of these objects.

Maybe I can solve the problem manually by lowering the connectors to a lower layer. But then why are they created the wrong way in the first place?

I attach the file that shows the problem