What do the checkboxes on the Tree mean in relation to the checkboxes on the lists?
The checkbox on the Tree (left hand side) shows the security status for all the Users/Companies and Classes selected in the lists. The checkboxes in the list (right hand side) show the status of the Users, Classes and Companies for object select in the Tree. This allows you to see two views from the one screen. For example, you can tell if “User1” has access to a particular object and then to see who else has access to that object.