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.