It's been quite a while since this was updated, but as i stumbled across it while hunting for a resolution to this issue, I'll post the fix that the OP left out.
to fix the issue. Zimbra's support later suggested to me:
/opt/zimbra/java/bin/keytool -import -alias new -keystore /opt/zimbra/java/jre/lib/security/cacerts -storepass ******** -file /opt/zimbra/ssl/zimbra/commercial/commercial.crt
Which is more... zimbrified, easier to use, and probably the beter choice.
/opt/zimbra/bin/zmcertmgr addcacert /opt/zimbra/ssl/zimbra/commercial/commercial.crt