DFS - Decommisioning Old Server

Hi,

Our domain functional level is 2003 and has to remain as this for the time being.

We need to decommission our DFS Root Server (2003) and migrate DFS to an existing 2008 R2 box.  The DFS role is installed on the new 2008 R2 server and can view the existing namespaces.  However,  if we disable the DFS Service on the old server, some  of the namespaces appear with a red cross and "The namespace cannot be queried.  The RPC server is unavailable". 

Can someone please advise the best way to migrate and establish a functional DFS environment on a new server?

Any help would be much appreciated.

Thanks