Disk usage randomly spiking to 99%, causing lag etc.

So yesterday for some unknown reason i began experiencing uncontrollable frame loss in games like arma 2 and CS:GO (games i can usually run fine on max settings). I searched around for the problem and after a while of finding no answers and trying several anti virus programs i resorted to a factory reset.
After the reset and re-installing arma 2, i started arma and was running a graceful 70fps on max settings. This morning i woke up and got on arma just to see the frame loss i had yesterday back to bite me in the ass. I have searched my entire computer and the only thing that seems wierd is two things, when i go to backup files it says that i don't have a drive (i have backed files up before and it has never told me that my drive is gone), and that for some reason my disk usage will randomly go up to around 99% for a period of around 45-50 seconds.
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PC Specs:

Disk: http://puu.sh/iJWdz/f1ac907212.png

CPU: Intel i5 4690 3.6 GHz

GPU: gtx 660

RAM: 2x 4GB (8GB total)

Power Supply: 750w Corsair
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Programs Installed after factory reset:
uTorrent (uninstalled problem still occuring)
Steam
Teamspeak 3
Skype
DayZ Commander
Avast
Google Chrome
Arma 2
Arma 2 OA
Arma 2 DayZ Mod
Counter Strike : Global Offensive
Dirty Bomb
Terraria
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Screenshots of Task Manager when CPU usage hits high:
(these are both at the same time, one is the top half other if the bottom half)

Top: http://puu.sh/iJW62/431673f229.png

Bottom: http://puu.sh/iJW6Y/ce7eab7bd4.png

Any help would be appreciated

check and fix bad sectors on your disk. In the command prompt, type in the following command: chkdsk /f /r and press enter. “/f” means to fix errors on the disk and “/r” means to locate bad sectors and recover readable information. After this process is done, try system restore again.