This is actualy a GDM bug, GDM does not pick up on your change in the default keyboard layout. To prove this (and workaround the issue) Remove the keyboard layout that you chose during the install, at the login screen the keyboard layout you chose will be selected, change this to the new default, the layout you chose during installation will not come back. You can also reverse the process, log out, change the keyboard layout in gdm, and the layout you chose in gdm will show up in your layouts.
This is actualy a GDM bug, GDM does not pick up on your change in the default keyboard layout. To prove this (and workaround the issue) Remove the keyboard layout that you chose during the install, at the login screen the keyboard layout you chose will be selected, change this to the new default, the layout you chose during installation will not come back. You can also reverse the process, log out, change the keyboard layout in gdm, and the layout you chose in gdm will show up in your layouts.