GPO only applying User Configuration settings

I have 2 OU's containing computer objects and 3 GPO's linked to these OU's. One OU for the student user accounts, one for the faculty user accounts, and one for the IT Department user account. You can see this in the image below:

You can also see in this image that I have the Security Filtering set so that the GPO only applies to the respective Security Group. These Security Groups have Read and Apply Group Policy permission settings. When I log in as one of the student users and run gpresult /z I get the following:

    Applied Group Policy Objects
    -----------------------------
        N/A

    The following GPOs were not applied because they were filtered out
    -------------------------------------------------------------------
        Local Group Policy
            Filtering:  Not Applied (Empty)

        Default Domain Policy
            Filtering:  Disabled (Link)

        Policy Refresh Settings
            Filtering:  Not Applied (Empty)

    The user is a part of the following security groups
    ---------------------------------------------------
        Domain Users
        Everyone
        BUILTIN\Users
        NT AUTHORITY\INTERACTIVE
        CONSOLE LOGON
        NT AUTHORITY\Authenticated Users
        This Organization
        LOCAL
        Students
        Medium Mandatory Level

It sees that the user is a member of the Students group, but it doesn't show the Students Configuration GPO at all. When I log in and look at the settings on the computer, the pop up blocker settings are set correctly (User Configuration), but when I go to look at any of the Computer Configuration settings they are not there. It's only applying the User Configuration settings. When I try to log in under an IT Department user the same thing happens. Any ideas what might be wrong?

I really need to get this working as some of our software requires some Firewall permissions and out IT Department needs the Restricted Groups feature to work so they can work on the computers when they go out to each Department to do a work order.