So just to add it seems that the 2nd IPA server hasn't managed to get the subCA 
cert & key as when I check the nssdb they aren't present on the 2nd IPA server. 
(See below)

Running the command as my own user
/usr/libexec/ipa/ipa-pki-retrieve-key "caSigningCert cert-pki-ca 
dd4ea812-c044-41c0-93bf-ec376c732c93" man-fb-ipa-01.testhost.com
returns with what looks like a JSON response with certificate and wrapped_key 
attributes which corespond to the subCA.

The question now is why does dogtag not get a response / thinks that it did not 
get a response?

Master IPA Server
certutil -L -d sql:/etc/pki/pki-tomcat/alias
Certificate Nickname                                         Trust Attributes
                                                             SSL,S/MIME,JAR/XPI

ocspSigningCert cert-pki-ca                                  u,u,u
subsystemCert cert-pki-ca                                    u,u,u
caSigningCert cert-pki-ca dd4ea812-c044-41c0-93bf-ec376c732c93 u,u,u
caSigningCert cert-pki-ca                                    CTu,Cu,Cu
auditSigningCert cert-pki-ca                                 u,u,Pu
Server-Cert cert-pki-ca                                      u,u,u

Replica IPA Server
certutil -L -d sql:/etc/pki/pki-tomcat/alias

Certificate Nickname                                         Trust Attributes
                                                             SSL,S/MIME,JAR/XPI

ocspSigningCert cert-pki-ca                                  u,u,u
subsystemCert cert-pki-ca                                    u,u,u
caSigningCert cert-pki-ca                                    CTu,Cu,Cu
auditSigningCert cert-pki-ca                                 u,u,Pu
Server-Cert cert-pki-ca                                      u,u,u
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