I am having exactly the same problem.
Version : Release 6.0.8_GA_2661.RHEL5_64_20100820052503 CentOS5_64 FOSS edition.
[root@archive ~]# mv /opt/zimbra/ssl/zimbra /opt/zimbra/ssl/zimbra_old
[root@archive ~]# /opt/zimbra/bin/zmcertmgr createca -new
** Creating directory /opt/zimbra/ssl/zimbra
** Creating directory /opt/zimbra/ssl/zimbra/ca
** Creating directory /opt/zimbra/ssl/zimbra/server
** Creating directory /opt/zimbra/ssl/zimbra/commercial
** Creating /opt/zimbra/ssl/zimbra/ca/zmssl.cnf...done
** Creating CA private key /opt/zimbra/ssl/zimbra/ca/ca.key...done.
** Creating CA cert /opt/zimbra/ssl/zimbra/ca/ca.pem...done.
[root@archive ~]# /opt/zimbra/bin/zmcertmgr deployca
** Importing CA /opt/zimbra/ssl/zimbra/ca/ca.pem into CACERTS...done.
** Saving global config key zimbraCertAuthorityCertSelfSigned...failed.
** Saving global config key zimbraCertAuthorityKeySelfSigned...failed.
** Copying CA to /opt/zimbra/conf/ca...done.
[root@archive ~]# /opt/zimbra/bin/zmcertmgr deployca
** Importing CA /opt/zimbra/ssl/zimbra/ca/ca.pem into CACERTS...done.
** Saving global config key zimbraCertAuthorityCertSelfSigned...failed.
** Saving global config key zimbraCertAuthorityKeySelfSigned...failed.
** Copying CA to /opt/zimbra/conf/ca...done.
[root@archive ~]# /opt/zimbra/bin/zmcertmgr createcrt -new
** Creating /opt/zimbra/conf/zmssl.cnf...done
** Backup /opt/zimbra/ssl/zimbra to /opt/zimbra/ssl/zimbra.20111214161813
** Generating a server csr for download self -new -keysize 1024
** Backup /opt/zimbra/ssl/zimbra to /opt/zimbra/ssl/zimbra.20111214161813
** Retrieving Commercial CA cert from ldap...failed.
** Creating server cert request /opt/zimbra/ssl/zimbra/server/server.csr...done.
** Saving server config key zimbraSSLPrivateKey...failed.
** Signing cert request /opt/zimbra/ssl/zimbra/server/server.csr...done.
[root@archive ~]# /opt/zimbra/bin/zmcertmgr deploycrt self
** Saving server config key zimbraSSLCertificate...failed.
** Saving server config key zimbraSSLPrivateKey...failed.
** Installing mta certificate and key...done.
** Installing slapd certificate and key...done.
** Installing proxy certificate and key...done.
** Creating pkcs12 file /opt/zimbra/ssl/zimbra/jetty.pkcs12...done.
** Creating keystore file /opt/zimbra/mailboxd/etc/keystore...done.
** Installing CA to /opt/zimbra/conf/ca...done.
The following resource have proven to be useless thus far:-
Administration Console and CLI Certificate Tools - Zimbra :: Wiki fix 1 year LDAP expiration error ZCS 6 New self SSL [SOLVED] New Cert install - LDAP "Unable to determine enabled services from ldap Mta fail and others bugs after trying to regenerate another certificate LDAP - Zimbra :: Wiki
Can anyone shed light on this problem?