Steps to reproduce
inkscape –version says Inkscape 0.48.4 r9939 (Jan 22 2014)
Have a look at the attached document

I've used avoid selected objects button of the connector tool on the blue star.
I've drawn a connector between the black rectangle and the 3D shape.
What you expected to see
When I close and open the document, I see that the connector between the black rectangle and the 3D shape avoids the star. The connector does not cross the star.
What you saw instead
When I close and open the document, I see that the connector between the black rectangle and the 3D shape doesn't avoid the star. The connector is drawn over the star.