If this check box is selected, every time the system is restarted FreshStart will scan through the system folder looking for files to move. If a file is either an INIT, or a file controlled by a redirection, the file will be moved to an appropriate folder. For example, startup documents will be moved to the Startup Documents Folder.
If you do not have this check box selected, but do have the appropriate folders created, FreshStart will scan the folders for INITs to execute. Additionally, if the Chooser or Control Panel Documents folders exist, these folders will be used as the source of files for the Chooser and Control Panel, respectively, regardless of the state of this check box. Documents in the system folder will be ignored by the Chooser and Control Panel.