Deactivating auto-security then reactivating it does require you to enter a different employee ID.  After a password is entered to reactivate auto-security under that ID, the screen will refresh the tools display to show which ones can be accessed and which cannot.  However, it doesn't necessarily refresh all of that employee's other preferences such as color theme or tool set (Favorites vs. All My Tools).  Therefore it's best to just log off and have the next user log in to completely refresh the home page.