I have seen issues where the template on the R2 boxes are using elliptical curve cryptography, basically if the template has a '#" charcter in it is what I think causes this process to be used. Try to use a template that doesnt have this in the front and then try to generate a cert against the template you created.
Here is a snip of the guide that I am forwarding you:
Determining Whether to Implement Cryptography Next Generation Algorithms
For Windows Server 2008–based version 3 certificate templates, the option exists to configure advanced cryptographic algorithms such as elliptic curve cryptography (ECC). Before configuring these settings, ensure that the operating systems and applications deployed in your environment can support these cryptographic algorithms.
http://technet.microsoft.com/en-us/library/cc731705%28v=ws.10%29.aspx
Screenshots in another article:
http://technet.microsoft.com/en-us/library/cc725621%28v=ws.10%29.aspx
Thanks,
Tarik Admani