To fix this, run the following command from the run window (Press WINDOWS KEY + R):
chkdsk c: /f
Once you are back in Windows, copy the Vista setup CD to a directory on your hard drive. From here, run the installation and choose "update". This will install Vista over the top of the current installation and fix any corrupt files.
It is recommended that you make a backup of any important data, as if this last step is performed incorrectly or goes wrong then you may lose your files.