MacBook Pro Starts Up Twice, Something is Wrong.

I know all of you guys will say that after a software update, the computer will start up 2 times. But then it happened after I installed the software update. The Launchpad works when you launch it, but the background doesn't blur out the wallpaper, instead it turns all gray. Mission Control doesn't work at times, since all the programs go missing when you swipe up with 4 fingers or launch the app manually. My computer is a solid state drive model and that when I start the computer it takes approx. 60 seconds to restart again, and once it restarts and I enter the password, it takes 5 seconds to boot. Might it be FileVault, or smcFanControl? These are the mods I've installed so far.

Result of turning filevault OFF was...
Normal behaviour. On restart, Double start up had stopped.
While filevault was turned off i also repaired permissions.
Restarted a couple of times and again, restart was normal.
Result of reverting Filevault to ON again was...
On restart, double start up again. Password entry twice. Chimes twice.
???? Hhmmmnnn.

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