System Preferences not being saved

I've set up Hot Corners with a modifier key, because my mouse cursor occasionally jumps around and ends up in the screen corners, where it would activate hot corners. However, suddenly yesterday (I think), the modifier key isn't being saved. The corner assignments are still the way they were. But the modifier key setting isn't "saved". I tried re-enabling the key settings. I'd click okay in the drop-down sheet, and then when I clicked the Hot Corners button again, the settings were there. Then, only a few hours later, the settings would be gone. It doesn't happen immediately.
In addition, I was on YouTube, and no matter where I clicked on the Mighty Mouse (now the Apple Mouse, I suppose) I get the right click menu. But where ever else I clicked on the page using the same location on the mouse, it was a normal left-click. When I disabled the secondary button in System Preferences (or rather, set both buttons as a primary button) it worked. But then the setting changed itself back to Secondary Button. What's going on?

Repair permissions and try deleting the com.apple.systempreferences.plist
~/Library/Preferences.

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