I had this strange behaviour on my Mac running OS X my Mac running OS X El Capitan 10.11.6.
When logging in, I have the following keyboard shortcut conflict between Spotlight and keyboard layout switcher:
After disabling it, conflict disappears:
But if I restart my Mac, the configuration was reset back to first step.
Same problem if I changed the keyboard shortcut: It was reset to default configuration after any restart, whatever the shortcut.
What is happening and why OS X isn't able to keep my keyboard preferences?