Your computer is always tracking internet activity and stores this information in your browser's cache, Temporary Internet Files and other areas on your hard drive.
ParetoLogic Privacy Controls is able to remove these files during a scan. However, many of these files are always being used by your operating system and cannot be cleaned until the computer is rebooted. After a scan Privacy Controls may prompt you to reboot if it detected any of these files.
In general, when your computer starts up again it rebuilds the files Privacy Controls had just removed, but without any sensitive data. When they are recreated, they will have the same name as the previous files that were removed but they will not contain the same information; they are empty and waiting for new data to be stored there. Occasionally if a large number of these files need to be cleared the results shown in Privacy Controls may be larger than expected. In the vast majority of cases this is nothing to worry about.