Comment 25 for bug 1215826

I was affected by the same problem and can confirm that removing indicator-keyboard fixes the problem, sadly sacrificing visual feedback about the current keymap though.

My entries at GSettings key org.gnome.desktop.input-sources.xkb-options were not lost during the update to 13.10 and started working again after removing the package. Besides 'ctrl:nocaps', I had also set 'grp:shifts_toggle', i.e. using pressing both shift keys together to toggle keymaps, and that shortcut was also restored by this.