It doesn't stick. But, rather than mess around with config files, I've got 
another work around. Put the command:
xmodmap -e "clear lock" -e "add lock = Caps_Lock"
into the sessions thingy (System-> Preferences -> Sessions -> Add, the name is 
whatever, the command is the one above etc.). 

Also after switching through the GUI, but before running the xmodmap
command, ctrl-alt-backspace has to use the 'real' ctrl key. ctrl-alt-
arrow (to switch desktops) has to use the 'new' (formally caps) ctrl
key.

After running the xmodmap command, the 'new' ctrl key works for
everything.

-- 
Caps lock LED changes state even when caps lock is mapped to ctrl
https://bugs.launchpad.net/bugs/173350
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