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.