Just thought I'd highlight this in case anyone else hits it.

NB: This was with a RapidSSL cert, not a self signed one.

I had an account which I migrated using the transfer tool, to another server, setup a new IP, etc... and discovered that the SSL cert for the domain wasn't working properly.

Not entirely sure what happened but it wasn't recognising the proper FQDN as the rightful cert owner.

Fix in the end turned out to be:

Main >> SSL/TLS >> Manage SSL Hosts
Locate the correct domain under "Installed SSL Hosts" and delete it.

.. then..
Main >> SSL/TLS >> Install a SSL Certificate and Setup the Domain

Put in the correct FQDN then reinsert all the private key, certificate and CA details from the original certificate and submit.

This seems to reset things and the certificate is now working as it should.