Comment 8 for bug 610248

From the GtkWindow documentation:

If you are saving and restoring your application's window positions, you should know that it's impossible for applications to do this without getting it somewhat wrong because applications do not have sufficient knowledge of window manager state. The Correct Mechanism is to support the session management protocol (see the "GnomeClient" object in the GNOME libraries for example) and allow the window manager to save your window sizes and positions.

Don't know where I got the idea that the window state is automatically saved by the window manager.