Recreating a Self-Signed SSL Certificate in ZCS 4.5 & 5.0
To clean up SSL certificate's and recreate a new self-signed cert try this:
as root:
rm -rf /opt/zimbra/ssl
mkdir /opt/zimbra/ssl
chown zimbra:zimbra /opt/zimbra/ssl
su - zimbra
keytool -delete -alias my_ca -keystore /opt/zimbra/tomcat/conf/keystore -storepass zimbra
keytool -delete -alias tomcat -keystore /opt/zimbra/tomcat/conf/keystore -storepass zimbra
zmcreateca
zmcreatecert
zmcertinstall mailbox ssl/ssl/server/server.crt ssl/ssl/server/server.key
zmcertinstall mta ssl/ssl/server/server.crt ssl/ssl/server/server.key