Removing right-command as "show desktop"
For those who like me didn't find the right answer ;-).
I accidentially turned on "Show desktop" on left "Command" key.
It has nothing to do with "Keyboard shortcuts" preference!

Go to "Preferences" -> "Mission Control" and change "Show Desktop" key from listbox to something useful.

Remember even if it doesn't show "left Command" key it uses it ;-), so change it.