After each scan, ParetoLogic Privacy Controls advises the user that it needs to reboot the computer in order to complete the cleaning of privacy files:

Privacy Controls cleans privacy information stored in areas such as Temporary Internet Files, caches, index.dat files, etc. Many of these files are continually being used by the operating system itself (Windows) and cannot be deleted while in use. In order to clean these files Windows must be restarted. When the computer is restarting, Windows will shut down and in that time will not be using any files. This allows the in-use files to be removed by Privacy Controls.

If Privacy Controls Reports It Has Not Cleaned All Items:

If the "Restart Later" button is selected at the end of a Privacy Controls scan or the "ParetoLogic Privacy Controls" dialogue box is moved so that the cleaning results are visible, you may notice that some items were not removed.

The "item(s) not removed" section indicates those files that are continually being used by Windows and cannot be deleted while in use. You can choose to either "Reboot Now" or "Reboot Later". If the "Reboot Later" option is selected, the remaining files will be removed the next time you restart your computer.