I've struggeled with the same problem. My suggestin is - try to install the cert using CLI command zmcertmgr. I installed my commercila cert from Verisign. I think it should be similar procdure for godaddy.
1. Backup commercial.csr and commercial.key.
2. Stop zimbra
3. Remove all from /opt/zimbra/ssl/zimbra/ca/* and /opt/zimbra/ssl/zimbra/commercial/*
4. Copy backuped commerccommercial.csr and commercial.key to /opt/zimbra/ssl/zimbra/commercial/
5. Copy cert you'v download from Godaddy to /tmp
$cp godaddy_cert.crt /tmp/commercial.crt
6. Download root cert (CA) and intermediate cert from Godaddy (I found a bunch of the certs on Verisign I hope Godaddy has the same)
7. Copy root CA and Intermediate cert to /tmp as one file:
$cat ca_root.crt ca_intermediate.crt > /tmp/ca_chain.crt
8. Verify the cert chain:
$sudo /opt/zimbra/bin/zmcertmgr verifycrt comm /opt/zimbra/ssl/zimbra/commercial/commercial.key /tmp/commercial.crt /tmp/ca_chain.crt
If chain is OK, you'll get a message like:
"“** Verifying /tmp/commercial.crt against /opt/zimbra/ssl/zimbra/commercial/commercial.key
Certificate (/tmp/commercial.crt) and private key (/opt/zimbra/ssl/zimbra/commercial/commercial.key) match. Valid Certificate: /tmp/commercial.crt: OK
”
If you have eror messages, it means the certificate path or chain is broken and you are missing certificate files. In most cases the intermediate cert is the path or chain that is affected. For more info on certificate path verification, please take a look at
Cryptography Tutorials - Herong's Tutorial Notes - OpenSSL - Certification Path and Validation
9. Create Self-Sign CA files
$sudo /opt/zimbra/bin/zmcertmgr createca
New files ca.pem, ca.key, zmssl.cnf will be created in /opt/zimbra/ssl/zimbra/ca/ folder
10. Install the commercial certificate with the command
$sudo /opt/zimbra/bin/zmcertmgr deploycrt comm /tmp/commercial.crt /tmp/ca_chain.crt
11. Verify the certificate was deployed
$sudo /opt/zimbra/bin/zmcertmgr viewdeployedcrt
12. Fix /opt/zimbra permissions
$sudo /opt/zimbra/libexec/zmfixperms
13. Start Zimbra