If I'm reading the patch correctly, it seems that you're changing the
response types in the buttons but not in the actual dialog response
handling.

dialog = self.gtk.MessageDialog(parent=self.window_main,
                                         type=self.gtk.MESSAGE_WARNING,
-                                        buttons=self.gtk.BUTTONS_YES_NO,
+                                        buttons=self.gtk.BUTTONS_NONE,
                                         message_format=msg)

The response types were GTK_RESPONSE_YES and GTK_RESPONSE_NO before..

+       dialog.add_button(self.gtk.STOCK_CANCEL, self.gtk.RESPONSE_CLOSE)
+       remove = dialog.add_button(self.gtk.STOCK_OK,self.gtk.RESPONSE_YES)

And here the buttons added use GTK_RESPONSE_YES and GTK_RESPONSE_CLOSE.

-- 
Ambiguous wording in confirmation alert box
https://bugs.launchpad.net/bugs/349336
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