GE60 ONC - HDD scratching all the time but HDD usage near 0%!

Hello to all!
I recently bought an MSI GE60 ONC.
I started the computer by running Windows 8 OEM. Then my nightmare began.
1/ Waited almost 2 hours to DL Windows Update (60 upgrades found)
2/ Extremely HIGH HDD usage was encountered 100% when using WU...
3/ After all updates where done HDD usage at 0% down to 100% so I tought the problem was solved.
4/ Now when starting my computer the HDD usage seems ok BUT my HDD is still scratching all the time as if he was working... I'm sitting on the desktop doing nothing but the HDD is always working.
And now I heard a litle weird noise every 5 min.
Refreshing Windows 8 with F3 DONE
Installing Windows 8 with F3 DONE
Help!
PS: Sorry if my english is weird it is not my first language.

how much system RAM you got?
and yes HDDs are not much fastern and they N1 units which slow down systems.

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