Notification Area Settings not staying after reboot

I have 2 issues with the notification area and trying to get settings to stay after restarting the computer. My office is deploying its first year of Windows 7 Pro systems and we make an excessive use of the Group Policy feature "Run only allowed Windows Applications."

My first issue with the notification area comes to quick access to the management utility. If I click the arrow to view all of the hidden icons and click the Customize option, I get the message that the "Administrator has prohibited the use..." of that feature. I can go to the control panel and access the notification area through there though. I have also elevated my user rights to administrative for unrestricted access to get to the menu from either the Customize option or control panel.

Now no matter which method I use to get to the notification area options, I can make the necessary changes and updated, I see the icons that I want to see and hide the ones that I don't want to see. After I restart the computer and sign back in, all of the notification area icons are right back to how they were before I made my customizations, and I can't figure out how to prevent this from happening. Any ideas?