I've had for a long time a 2003 AD Root CA in the domain and Admins have been able to request certificates to this CA through IIS interface without the need to generate a request file using the Create Domain Certificate feature.
Recently I added a new 2008 R2 AD Root CA in the domain and the root certificate has been propagated to the whole network as a trusted Root CA certificate.
If I go to IIS on any server or my local computer the new CA is not listed when trying to create a new domain certificate.
My AD DS functional level is 2003
Both CAs are NOT domain controllers
Can someone lead me to find a solution