When a permissions analyses is initiated, users have the option of including only objects with unique (non-inherited) permissions or objects with both inherited and non-inherited permissions. Having Show unique permissions only selected is the ControlPoint default.
ControlPoint Application Administrators can, however, change the default (so that Show Unique Permissions Only is unselected) by changing the parameter value of the ControlPoint Configuration Setting "Show unique permissions only" Default Value from true to false.