Phil - Your question about this problem is a good one. I also experienced the 
exact same thing. I had placed a few web sites into the "Trusted Sites" in the 
GPO and wham! I could no longer see the GPO, in my GPMC. I also could not see 
any of my users when I did an RSOP. I searched the internet with very little 
help except that many others were having the same issue. I finally came across 
a bit of help, check out the solution I found:

Trusted Sites Problem

•       When I apply ‘Trusted Sites’ policy to the GPO: User Configuration / 
Windows Settings / Internet Explorer Maintenance / Security, the GPO will not 
show up on the MMC. Also I cannot see any GPO settings for any users who have 
this policy applied to their user configuration.
•       As soon as I remove the policy, the user configurations show up fine.
•       I am testing another way to add to the ‘Trusted Sites’, by using: User 
Config\Admin Templates\Windows Components\Internet Explorer\Internet Control 
Panel\Security Page\ 
Policy: Site to Zone Assignment List 
Any site you add to the list with a value to 2, with be in the trusted sites 
zone. 

This actually works. Hopefully this will work for you.

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