System menu bar items missing/flashing after upgrade

Hi
I upgraded to Yosemite and my systems menus bar is missing/flashing occasionally. Only spotlight appears.
I have attached a screenshot of it.
Somehow, I can't use command + shift + 4 to take screenshots anymore, so used Grab instead.

I should also mention that this started recently, which is about 2 weeks after Yosemite update so I am guessing it's not caused by the upgrade.
I tried logging onto the Guest User account to see if the same happens, and found out that it does not happen in Guest Account.

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