I think I have the same problem:
After changing the hostname in every location I know of and rebuilding the security thing, thereīs still a message when opening webmail: "You are connecting to 'oldhostname.com' but certificate belongs to 'newhostname.com'...". The 'oldhostname' ist the name the server had when I made the installation. So there must be another location (or more than one?) where the old name is stored. I could even just reinstall ispconfig but Iīm not sure if that would help because an upgrade usually touches not all config files (hmmm, thatīs why itīs called an upgrade, isnīt it?