I also receive this message when software-center is reconfiguring. But i have X 
display ( i think )
: /usr/lib/py modules/python2.6/gtk-2.0/gtk/__init__.py:57: GtkWarning: could 
not open display warnings.warn(str(e), _gtk.Warning

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Prints warnings during installation without an X display
https://bugs.launchpad.net/bugs/61134
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