New hard drive - Disk Permissions not working

Recently had my Hard Drive relplaced, and while updating ran in to multipul issues.
The main one being with iTunes, I can't download songs I purchased from my iPhone & when I try to do it manually it tells me the my permissions need to be changed. So I ran a permissions verification on DiskUtility and it's telling me a whole bunch of stuff doesn't match up.
Should I run a repair?
Any other ideas?
Also, my last hard drive had no issue installing Mountain Lion, and this one refuses.
Any one else have this issue? 

MK6475GSX
Yes, that has AFT. See MKxx75GSX.
I uploaded all the drivers..
But the point is that when you restore the hard disk to its original out-of-the-box contents using Toshiba recovery media, all the drivers are already properly installed. Everything should work as it originally did.
I would perform the restore again and immediately install this driver.
   Intel Rapid Storage Technology
-Jerry

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