ok, that was a gtk bug, it has been fixed in trunk:
http://git.gnome.org/browse/gtk+/patch/?id=f9d77959a4518699a96b3c85ddc18d0ff01aeac5
I backported the fix and uploaded to quantal-proposed
** Changed in: gtk+3.0 (Ubuntu Quantal)
Status: Triaged => Fix Committed
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https://bugs.launchpad.net/bugs/1047431
Title:
gedit and evince hits BadWindow XErrors when run from different
"contexts" with GTK 3.6
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