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.