Configuring Jenkins with StartSSL - adding the issuer chain
I had a similar problem and after some research what got everything to be trusted was :
Merged the intermediate authority certificate and
<mydomain.crt file>into 1 unified certificate calledmerged.cerusing the link you mentioned(From: https://serverfault.com/questions/569866/jenkins-wont-serve-with-ca-signed-certificate)
openssl pkcs12 -inkey /location/to/key.pem -in /location/to/merged.cer -export -out keys.pkcs12keytool -importkeystore -srckeystore keys.pkcs12 -srcstoretype pkcs12 -destkeystore jenkins.jks
NOTE: the key to use for the merged.cer should be the same as <my private key file>
Then follow the Jenkins Wiki to use the KeyStore instead of the certificate
java -jar jenkins.war --httpPort=-1 --httpsPort=8080 --httpsKeyStore=/path/to/jenkins.jks --httpsPrivateKey=<my private key file>