If you run chkdsk againt an NTFS volume, it may report that it found problems:

C:\>chkdsk c:
   The type of the file system is NTFS.
   Volume label is System.

   WARNING! F parameter not specified.
   Running chkdsk in read-only mode.

   chkdsk is verifying files (stage 1 of 3)...
   File verification completed.
   chkdsk is verifying indexes (stage 2 of 3)...
   Index verification completed.
   chkdsk is verifying security descriptors (stage 3 of 3)...
   Security descriptor verification completed.
   Windows found problems with the file system.
   Run chkdsk with the /F (fix) option to correct these.
If you then schedule a chkdsk /f, shutdown and restart, your Application Event log may contain something like:
   Event Type:     Information
   Event Source:   Winlogon
   Event ID:       1001
   Computer:       Computer_Name
   Description:    Checking file system on C:
                   The type of the file system is NTFS.
                   Volume label is System.

   A disk check has been scheduled.
   Windows will now check the disk.                        
   Cleaning up minor inconsistencies on the drive.
   Cleaning up 153 unused index entries from index $SII of file 0x9.
   Cleaning up 153 unused index entries from index $SDH of file 0x9.
   Cleaning up 153 unused security descriptors.
   Windows has made corrections to the file system.
When you remove a file or folder that had 'custom' permissions, the ACL is not deleted, it is cached. Chkdsk /f removes ACLs that are no longer used.

This is normal behavior and does NOT indicate a problem with your file system.