Maybe you have corrupt filesystem? You can try to repair [From a Windows Installation Image] using the repair utilities you can get a command prompt and run the command:
chkdsk /r
Which will find and repair bad sectors and meta data on the filesystem
If this doesn't fix then you can proceed [carefully] with data recovery tools:
1) Always make an image first. Then try to recover files from the image. Never work directly from the HDD as you may accidentally delete/overwrite some stuff unintentionally. [or if you feel brave, at least mount your hard drive as read only)
Usually I make an image with 'ddrescue'
2) Use recovery programs like 'foremost' or 'photorec' on the image.
The Ubuntu Wiki has a nice article on using these kinds of tools
https://help.ubuntu.com/community/DataRecovery