Run CHKDSK in readonly mode. Do not allow it to "fix" anything. This will tell you if there are any file system problems.
If you suspect that your drive may have bad sectors, try a comprehensive SMART diagnostic. Look for reallocated, pending, or uncorrectable sectors.
HD Sentinel (DOS / Windows / Linux):
http://www.hdsentinel.com/
HDDScan for Windows:
http://hddscan.com/
See this article for SMART info:
http://en.wikipedia.org/wiki/S.M.A.R.T.
The safest thing to do is to clone your drive, sector-by-sector, and then work on the clone.
Ddrescue or dd_rescue both know how to skip over bad patches in the media. They will clone the easy sectors on the first pass, and then try for the more difficult ones on subsequent passes. You can also clone the drive in reverse. This will effectively disable read lookahead caching.
http://www.gnu.org/software/ddrescue/ddrescue.html
http://www.garloff.de/kurt/linux/ddrescue/
Could we see the partition table and boot sector with Microsoft's Sector Inspector?
http://www.users.on.net/~fzabkar/SecInspect.zip
Extract the above archive to the one folder and execute the SIrun.bat file. The procedure will generate a report file named SIout.txt which you can then upload to a file sharing service so that we can examine it.