Ok So I did some research on the net for this one.
It can either be this:
1. Huge amounts of system restore space + files hidden in your system volume folder (very unlikely)
3. Harddrive is physically damaged
4. A huge part of your harddrive is corrupt.
I know this sounds completely generic, but i'd recommend doing chkdsk a couple more times. This time go to my computer, right click your C:/ drive, click properties Tools tab
Click Check Now
click both boxes and restart.http://www.hardwareanalysis.com/content/topic/69352/
Also download this and run a scan and give me a screen cap of it.http://www.sixty-five.cc/sm/