Apple Menu items are missing. How do I restore them?

My Apple Menu is missing some items. Not sure of all that may be missing, but the ones that I use that are missing include "System Preferences," "Restart," and "Shutdown."
System Preferences is still installed and available from the Applications folder, and I can restart or shutdown the system in other ways, but I'd sure like to get those items back on the menu.
I'm not what caused this, but I did some system maintenance including an iDefrag full defragmentation and some tweaking in Onyx. Can't say I know at which stage this happened, but the system seems to be behaving normally but for the missing items.
System is a Macbook Pro 17-inch, Mid 1009, running OS X Mavericks 10.9.2.
Thanks for any advice you can offer.

As it turned out, restarting the system didn't help, but shutting down and starting again did. Not sure if there's a difference between a restart and a shutdown+start, but I know there is a slight difference between a warm boot and a cold boot on PC, so maybe there is.
Anyway, the problem solved without major surgery. This specific option of removing the System Preferences menu item isn't available in Onyx, though removing the Restart and Shutdown options are (which I did not select). So, I guess I'll chock this up to an anomaly.
Thanks for the help guys.

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