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.