If you check your hard drive with Gparted, you will notice that it will have a Yellow warning mark in any of your NTFS partitions. The way to fix it is shutting down totally Windows (no hibernation, no suspend, but correct shutdown of the system). If that doesn't get rid of the warning, you should run chkdsk /f in cmd (just type cmd in the start menu) with Administrative Privileges and restart Windows twice.
In case of Windows 8, apart of the actions above, you should disable Fast Boot and shutdown the system.