I can confirm this on HP Deskjet 6840. Printing from evince, gedit, evolution is not recognizing the activated duplex. If it is activated through CUPS Webinterface duplex is working in these apps too. So it must be a problem with communication between cups and gnome-print.
-- [evince duplex] GNOME doesn't follow print configuration https://launchpad.net/bugs/39871 -- desktop-bugs mailing list desktop-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/desktop-bugs
