Oh, this is tickling a memory.
Somewhen ago, we were migrating our database somewhere. (From colocated to remote? Was it that long ago?) Doing this required updating the MSSQL version in the old location so that the database would be peer with the new version on the new server. But we ran into a mysterious error in the MSSQL installer. Turns out that was a known issue that had a patch (or workaround).
BUT… the core issue was that the server’s original system name – from being deployed as a Windows VM from a template – was embedded in a table somewhere.
Probably not related to your certificate issue, but I remembered it.