What brand and model hard drive are you using? You should download the manufacture's diagnostics tool to ensure your sectors have not been corrupted by physical means before proceeding further.
For Western Digital:
http://download.wdc.com/windlg/WinDlg_v1_29.zip
For Seagate: http://www.seagate.com/support/downloads/item/seatools-win-master/
For Other Manufactures: Google is your friend!
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If it detects physical damage, I suggest backing up
Immediately, then replacing the drive; you will most likely have data loss if this is the case unfortunately (unless the physical damage was on an unused portion of the drive).
Otherwise if is only soft-based damage, you can attempt to correct the sectors via windows checkdisk:
(Back Up the Drive First!)
open your My Computer window, right click the damaged disk, select "Properties," select the "Tools tab, under error checking, select "Check Now."
If this is your main boot drive, you will need to restart your computer in order for the checkdisk to run.
Re-run the diagnostic software after the checkdisk completes. If there are any abnormalities, check back here and we can try some other steps.