ADCS / New CA / Chicken or Egg?

Hello,

I am fairly knowledgeable about PKI and ADCS, but have a few question about AD behavior after we created a new sub CA.

We have a two tier PKI with an offline root, and two subordinate CAs. These have been around for several years, and we have had minimal problems. Our CAs are nearing the end of their lifecycle, so we recently provisioned a new sub CA.

We installed the role on the new server, got the offline request signed by the root, and completed the install. I am assuming that when you install the CA certificate onto a new enterprise subordinate CA, it goes ahead and publishes a bunch of stuff to the various AD containers relating to PKI (Certificate Authorities, Enrollment Services, NTAuth, CDP, AIA, etc. This is probably why you need EA permissions on the domain to complete the install.)

Anyway, we completed the install and started the CA service. Immediately, the DCs auto-enrolled for the Kerberos Authentication Template. This is not necessarily a bad thing, as we use Smart Card Login (SCL) and the DCs need to have a certificate issued by the new CA.

Almost immediately, we began seeing an error when attempting to RDP or login stating "An Untrusted Certification Authority was detected while processing the domain controller certificate used for authentication" and users were kicked back to login. UN/PW/2FA worked, so we were not totally sunk.

The issue gradually cleared itself up over the course of a few hours. 

My theory is that not all workstations and servers immediately got the new CA cert, which would have been propagated through routine GP updates, and that when windows saw domain controllers presenting untrusted domain controller certs, they balked at it. Either that, or the clients were seeing an untrusted cert in NTAuth.

So what is the best way to mitigate this? Remove all certificate templates from the new CA before you turn the service on? Let the new CA cert propagate around before you start issuing DC certs?

Thank you for the insight!