Your CS.cfg file looks odd to me, but it could be the lower version you're 
running or some manual changes made at sometime.

--->8---
grep internaldb.ldap /etc/pki/pki-tomcat/ca/CS.cfg 
------------------------------
internaldb.ldapauth.authtype=SslClientAuth
internaldb.ldapauth.bindDN=cn=Directory Manager #AFAIK this should be 
pkidbuser's DN
internaldb.ldapauth.bindPWPrompt=internaldb
internaldb.ldapauth.clientCertNickname=subsystemCert cert-pki-ca
--->8---

FreeIPA uses ldap as the backend for pki-tomcat, it it uses the ldapauth cert 
you have listed to look for a UID that has a matching userCert value (more to 
it, but this sums it up)

I believe you might want to try and use the pkidbuser DN instead of the 
Directory Manager DN as that would produce the proper match for you. 

I would also verify that the CA that signed your subsystemCert exists in your 
dirserv ldap nssdb in /etc/dirsrv/slapd-DOMAIN.NAME. If it doesn't exist 
install it using pk12util and set trust on it with certutil. 

Hopefully this helps.
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