Q: I've upgraded toR2, so why aren't I seeing new Server 2012 R2 and Windows 8.1 Group Policy settings?
A: Each machine has a local policy store which consists of the ADML and ADMX files that make up Group Policy settings. These are located at C:\Windows\PolicyDefinitions.
If you have upgraded but don't see the new Windows Server 2012 R2 Group Policy settings, then most likely you have configured a central policy store which would not have been updated. A central policy store is located in the SYSVOL share of all domain controllers (DCs) in a domain, enabling a consistent set of policy definitions to be used throughout the domain.
You can check which policy definitions the Group Policy Management Editor is using by viewing the full detail of Administrative Templates section heading, as shown in the screen shot below:
As you can see in the screen shot, this editor is using the central store for definitions.
To update the policy files in the central store copy the content from C:\Windows\PolicyDefinitions on a Windows Server 2012 R2 DC to location \\<domain>\SYSVOL\<domain>\policies\PolicyDefinitions.
As an example, this is the location I would use for updating my policy files: \\savilltech.net\SYSVOL\savilltech.net\policies\PolicyDefinitions.