Well, with 6.0.8 things seem to have worsened a little, with random behaviour. Still error, even if different message, but sometime everything seems OK after a restart, sometime everything is blocked due to wrong certificate
mxz:~# /opt/zimbra/bin/zmcertmgr createca -new
** 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.
mxz:~# /opt/zimbra/bin/zmcertmgr createcsr self -new
** Generating a server csr for download self -new
** Creating /opt/zimbra/conf/zmssl.cnf...done
** Backup /opt/zimbra/ssl/zimbra to /opt/zimbra/ssl/zimbra.20100827235107
** Retrieving Commercial CA cert from ldap...done.
** Creating server cert request /opt/zimbra/ssl/zimbra/server/server.csr...done.
** Saving server config key zimbraSSLPrivateKey...done.
mxz:~# /opt/zimbra/bin/zmcertmgr createcrt -new -days 3650
Validation days: 3650
** Creating /opt/zimbra/conf/zmssl.cnf...done
** Backup /opt/zimbra/ssl/zimbra to /opt/zimbra/ssl/zimbra.20100827235136
** Generating a server csr for download self -new -keysize 1024
** Creating /opt/zimbra/conf/zmssl.cnf...done
** Backup /opt/zimbra/ssl/zimbra to /opt/zimbra/ssl/zimbra.20100827235136
** Creating server cert request /opt/zimbra/ssl/zimbra/server/server.csr...done.
** Saving server config key zimbraSSLPrivateKey...done.
** Signing cert request /opt/zimbra/ssl/zimbra/server/server.csr...done.
mxz:~# /opt/zimbra/bin/zmcertmgr deploycrt self
** Saving server config key zimbraSSLCertificate...done.
** Saving server config key zimbraSSLPrivateKey...done.
** 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...unable to load certificate
19889:error:0906D06C:PEM routines:PEM_read_bio:no start line

em_lib.c:650:Expecting: TRUSTED CERTIFICATE
done.
mxz:~# /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.
unable to load certificate
21323:error:0906D06C:PEM routines:PEM_read_bio:no start line

em_lib.c:650:Expecting: TRUSTED CERTIFICATE
#
Hope a kind Zimbra developer is willing to have a look at this mess
