Thanks Paul.
We discussed it in some length at the gtk-app-devel list, here:
http://mail.gnome.org/archives/gtk-app-devel-list/2008-May/msg00141.html
Turns out there's a designated way for the window to set a hint on itself that it shouldn't receive focus upon creation (gtk_window_set_focus_on_map()).
Oddly enough, Gnome does not seem to respect that hint. GTK+ being the default widget toolkit for Gnome, this looks like a bug.
Thanks,
Tom