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Deploying certificate via GPO and by VBScript/SCCM

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We have a web filter certificate that has been getting deployed by GPO for the last few months. While most computers are getting the policy/certificate, some just aren't. Running gpupdate /force processes the policies without error, but still does not install the certificate. 

So, I wrote a vbscript that will check the registry to see if the certificate is located in either HKLM\Software\Microsoft\SystemCertificates\Root\Certificates orHKLM\Software\Policies\Microsoft\SystemCertificates\Root\Certificates. If it not, the certificate will install into the Trusted Root Certification Authorities\Certificates container.

My concern is, if the computer does eventually get the certificate through GPO, it will list two of the same certificate in the Trusted Root container. My concern is, will this affect anything? The certificate doesn't expire until 2034, so that shouldn't be an issue.

We've looked at why these certificates aren't being applied via policy, but have not yet found a reason. Any guidance that can be offered would be appreciated. 



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