Windows Server 2008 R2 Certificate Authority does write certificates to configured AIA locations

I have a stand-alone root and enterprise issuing CA hierarchy. Both are configured with and AIA location to write a copy of the CA certificate to C:\Windows\system32\CertSrv\CertEnroll\<CaName><CertificateName>.crt

REG value below:

1:C:\Windows\system32\CertSrv\CertEnroll\%3%4.crt

When the certificate services is restarted, the certificate file written to the location is as if the default configuration was still in place. EG: C:\Windows\system32\CertSrv\CertEnroll\<ServerDNSName>_<CaName><CertificateName>.crt

Can this be fixed or do I need to manually create the file?