Sounds like you've made a real breakthrough on the scripts - which is fantastic.
No, I've not compiled yet. I doubt very much given the number of commits we are seeing currently, that there is a fix just happening to be in there.
I have traced a related issue back to August 2012 - https://github.com/fritzing/fritzing-app/issues/1953 which was fixed for breadboards, but I think female headers got overlooked, possibly because they didn't connect at all in those days. Unfortunately I cannot check the source. When the dev team imported the source they left out the history. The svn may still be on googlecode but if it is it's behind an impenetrable redirect.
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Spurious unrouted connections in BB view
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