The GUI keyboard is set up after you log in, because two people sharing a computer might want things done differently, so the keyboard layout for the log in has to be done separately. Have a look at this documentation:
Keyboard
Things may not be exactly the same for you — Arch uses /etc/X11/xorg.conf.d/10-evdev.conf while my PCLinuxOS has /etc/X11/xorg.conf.d/00keyboard.conf — but you should be able to find the file to edit.
For background,
Background
PS It does help if you specify your distro and GUI in your profile as I do.