Billzby
I ended up to just replace my hard drive. I put another hard drive which its specification was lower than the old one and slower but is running normal now. I am %100 sure that the old hard drive is healthy . I checked it several times with the pc check software which is one of the best hardware diagnose program and it passed all the tests. So at this stage i don't know why it stopped working normally. 
 

REZA
 Billzby
I ended up to just replace my hard drive. I put another hard drive which its specification was lower than the old one and slower but is running normal now. I am %100 sure that the old hard drive is healthy . I checked it several times with the pc check software which is one of the best hardware diagnose program and it passed all the tests. So at this stage i don't know why it stopped working normally. 
 

Thanks for the update. This whole thing is baffling me too. I bought a WD Black HDD which is better than what I have in there now and will try a 3 drive setup. Something is telling me though, that I will have to do what you did and just replace the HDD completely and use a 2 drive setup