This may be a Mac-only bug, I don't know.
When closing a window, maybeSave() is called to allow the user to save the changes, discard the changes, or cancel (i.e., stop closing the window and do nothing).
The "cancel" option doesn't work -- it creates an empty window.
The Qt Quarterly gives an example of how this can work:
http://doc.trolltech.com/qq/qq18-macfeatures.html
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Actually, here "cancel" does the same as "discard": nothing... Absolutely nothing changes.
This mean: On my OpenSUSE I have two options: Either save the file to disk or kill Avogadro...
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This is fixed in SVN, although I can't find what revision number. I'm currently at 929 -- it was fixed a few weeks ago.
I'm marking this closed.