Hi Kat7,
It is highly probable that the certificates issued by the DoD PKI do not contain the specific Microsoft proprietary SID extension (OID 1.3.6.1.4.1.311.25.2). Without this extension, the standard Subject/Issuer mapping (format X509:<I>Issuer<S>Subject) is technically classified as a "Weak" mapping. If your Domain Controllers are configured with the registry key StrongCertificateBindingEnforcement set to 2 (Full Enforcement), the KDC will reject these weak mappings immediately, resulting in Event 39.
To resolve this without waiting for a certificate reissue, you must manually create a "Strong" explicit mapping in the altSecurityIdentities attribute of the user object. The crucial detail is the format: you cannot use the Subject/Issuer string. You must use the SHA1-PUK (Thumbprint) or Issuer/Serial Number format to satisfy the strong binding requirement.
Please perform the following steps on the user's Active Directory object: Clear any existing entries in altSecurityIdentities that rely on <I> and <S> tags. Replace them with the specific SHA1-PUK format using the user's certificate thumbprint. The string must look exactly like this: X509:<SHA1-PUK>ThumbprintHexValue (Ensure there are no spaces in the hex string).
Alternatively, you can use the Issuer and Serial Number format, which is also considered strong: X509:<I>IssuerName<SR>SerialNumber
Once you apply this change, force a replication or wait for it to propagate to the authenticating DC. The KDC will recognize the <SHA1-PUK> or <SR> tag as a strong mapping method and allow the authentication to proceed even if the certificate itself lacks the SID extension. Regarding your mention of adding the thumbprint to a GPO, note that Group Policy is typically used to configure the enforcement level (Compatibility vs. Full Enforcement), not to list individual allowed thumbprints for mapping; the mapping logic resides strictly on the user object attributes or the Certificate Authority configuration.
I hope you've found something useful here. If it helps you get more insight into the issue, it's appreciated to accept the answer. Should you have more questions, feel free to leave a message. Have a nice day!
VP