Empty folders on Main Menu that go no where

We are on HCM 9.1, implementing Tools 8.54.  Our employees with basic security access to Self Service only are seeing folders that they have no access to.  We've reviewed the Permission List in the Employee Self Role and there is no access to anything under these other folders.  We've also verified the Employee Self Service Permission List are not on the Structure and Content Folder Security tab.  It seems to be related to changes to the base permission list PTPT1000 in the Tools upgrade that causes this to occur.

 

For example, we have employees who get access to PeopleTools on their menu but all of the menu items dead-end so they can’t actually do anything.