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I have lots of problem with inkscape connectors incluing these
1. when Icopy/pase a connector everything changed!
2. can not break a connector alone!
now I do not know how to creat some organizational chart like diagrams
Inkscape connector tool is very basic. You could try filing bugs at https://launchpad.net/inkscape.
In the short term if you're feeling hardcore you could experiment with something like GraphViz http://graphviz.org/About.php
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