Comment 21 for bug 486922

I had to reboot my box, so I've given theoretical Xsession.d code I described in #16 a try, and indeed setting it there does not work if you are using gnome-session, as for unknown reason gtk+2.0 refuses to pass variable down to applications it starts. So gnome-session itself uses native windows - which is of no use for you (it creates no windows itself), as you need gnome-panel and all other gnome apps started by gnome-panel to use native windows.

Rebuilding gtk+2.0-2.18.5-1 with attached patch, reinstalling built libgtk2.0-0, and setting value to 'inherit' is propagated correctly through whole hierarchy of GTK applications, so now 'export GDK_NATIVE_WINDOWS=inherit' in /etc/X11/Xsession.d/11petr works, and forces all gtk applications you start (and apps spawned by these apps) to use native windows.