I looked at the Chrome output of the three parts in the chain. They are identical to the cert.pem,chain.pem and the first part of the fullchain.pem. All of those files were issued today.
Where are you getting the information on the certificates supplied by the server? This is the only virtual server that is configured for https. The only other place that has a reference to a certificate is the ssl.conf file in the conf.d directory. That file refers to a default certificatte generated by the server when it was installed. I think the vhost file configuration overides that.
Thanks
Ernie