OS X keyboard preferences (click to enlarge)

Why won't my Mac reliably retain modifier key changes in preferences? As shown in the screenshot, I regularly make my CapsLock key into a control key. As an emacs user, that's much better for me. I was very glad when Apple added this as part of the OS. But about one out of three times OS X loses my preference at reboot. This doesn't happen with other preferences, so why this one?