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It looks like my server admin tools are adding the following unwanted settings to every GPO I touch.

Computer Configuration/Policies/Windows Settings/Security Settings/Local Policies/Security Options/Public Key Policies/Trusted Root Certification Authorities

Allow users to select new root certification authorities (CAs) to trust: Enabled

Client computers can trust the following certificate stores: Third-Party Root Certification Authorities and Enterprise Root Certification Authorities

To perform certificate-based authentication of users and computers, CAs must meet the following criteria: Registered in Active Directory only

It's causing weird problems like certain CAs stop being trusted by IE. What the heck is going on? I'm using the RSAT 2008 r2/Win 7 on a Win 7 x64 machine.

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The setting Computer/Policies/Administrative Templates/System/Internet Communication Management/Restrict Internet communication - Settings was doing this.

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