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.

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https://bugs.launchpad.net/bugs/1215826

Title:
  Lost ability to remap Caps Lock to Ctrl

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