I also had this problem, and it appears for the same reasons.  I had
installed xserver-xgl and then un-installed it, that is when the dialog
box started showing up.

I resolved it by changing the key in the configuration editor to match whatever 
was being detected by xserver.  In my case all I needed to do was change the 
following:
/desktop->gnome->peripherals->keyboard->kbd.sysbackup->model=pc101

to

/desktop->gnome->peripherals->keyboard->kbd.sysbackup->model=pc105

and that stopped the dialog from showing up.

-- 
gnome keyboard layout question at each login
https://bugs.launchpad.net/bugs/154401
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