Is there a version match between your Group Policy Object (GPO) containers and templates?
This PowerShell script will check that the version of each GPO is consistent in the Active Directory Group Policy Container (GPC) and on each Domain Controller in the Group Policy Template (GPT).
All Windows Operating Systems (since Windows 2000) will apply the GPO regardless of a version mismatch. However, a version mismatch will typically mean that some settings will simply not be applied because they haven’t been replicated correctly across the environment. Replication issues with good old flaky FRS and perhaps (but rarely) the newer DFS-R is often the reason that the GPT gets out of sync and lags behind the GPC. This is such a common problem.