I had the same problem (ie CapsLock and Ctrl not swapped after reboot), but unchecking the toggle button "Separate layout for each window" seems to have corrected the behavior.
As a side note, it seems that only starting gnome-keyboard-properties temporarily solves the problem (until reboot), so choosing the correct setting again is not really necessary.
I had the same problem (ie CapsLock and Ctrl not swapped after reboot), but unchecking the toggle button "Separate layout for each window" seems to have corrected the behavior.
As a side note, it seems that only starting gnome-keyboard- properties temporarily solves the problem (until reboot), so choosing the correct setting again is not really necessary.