Comment 1 for bug 1418939

I think the indicator-keyboard code for migrating settings is responsible, at least for the layout setting. I worked around it by writing a gschema override for org.gnome.libgnomekbd.keyboard.layouts, the old location where settings are migrated from, instead of org.gnome.desktop.input-sources.sources.

http://bazaar.launchpad.net/~indicator-applet-developers/indicator-keyboard/trunk/view/head:/lib/main.vala#L389