I think I might be experiencing this problem as well, though only my
left super key has stopped working.

s3a, could you please try running the following command in a terminal:

xev

pressing your super keys, and watch if the program writes something to
the terminal, and attach the output?

Also, could you post the output of the following command:

xprop -root

-- 
Super user key shortcut does not work (=get captured) when you try to use it in 
System --> Preferences --> Keyboard Shortcuts
https://bugs.launchpad.net/bugs/483113
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