zmcontrol does an LDAP query to see which services need to be started on a server. If the server entry does not contain the appropriate services then neither zmcontrol or /etc/init.d/zimbra will attempt to start them. All the services you speak of invovle the mailstore, you can use zmprov to see if LDAP knows what is installed and enabled.
zmprov gs mail.example.com | grep -i service ---- i think that will work. |