Group policy filtered to a group not applying to users

We are having a issue where the group policies filtered to a group are not applied to the users in windows 2012 domain. These policies used to work fine earlier. If we apply the same policy to authenticated users group then it applies fine.
This policy has user settings but is applied to server OU. Gpresult does not show this policy at all in applied user policy listing or denied list.
When I run modelling wizard it shows up but lists under denied due to filtering. And also complains about "ad / sysvol version mismatch". If I run Rsop for 1 user then it does not show the settings related to this policy.
Recently we moved the Pdc, infrastructure master and rid master roles  to a second DC. That was done to split the roles on 2 DCs as we have 3 DCs. Please let me know what can I look at to resolve the issue.
curious7Asked:
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Adam BrownSr Solutions ArchitectCommented:
If it has User policy settings in it, it needs to be linked to an OU that has user objects in it. Computer objects will not apply User Configuration policies unless policy loopback processing is enabled. If you want the GPO to only apply to users that log in to those servers, enable loopback policy processing. https://blogs.technet.microsoft.com/askds/2013/02/08/circle-back-to-loopback/ has good info on it, if that's what you're trying to do. Otherwise, you'll need to change your links so it is linked to an OU with the user objects you want it to apply to in it.
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CoralonCommented:
If it works with Authenticated Users, but not when you modify the security, then chances are excellent you are not adding Domain Computers back to the security.  Ultimately, the computer is what has to read in the GPO, and if you don't give it the rights, it can't read the policy, and therefore it does not apply.

Coralon
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Jeremy WeisingerSenior Network Consultant / EngineerCommented:
I agree with Coralon. User policies are read using the computer context of the computer the user is logged onto. If it used to work then stopped it is because this is a recent change from Microsoft. In June Microsoft released a patch that changed how the policy is retrieved from the user context to the computer context. You can read more about it here: https://blogs.technet.microsoft.com/askds/2016/06/22/deploying-group-policy-security-update-ms16-072-kb3163622/
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Adam BrownSr Solutions ArchitectCommented:
The answers given here do adequately answer the question together. If the GPO (which has user settings in it) is linked to an OU that contains computer objects (as was mentioned), Loopback Policy Processing is required, which is what I recommended. The other answers note that the computer objects need to be included on security filtering to apply the GPO as well. The answers given provide either part of or the entire solution for the explained issue and should be credited.
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CoralonCommented:
Comments did provide the correct information to resolve the issue.
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