I figured I would start a new thread as the last one was fixed.
It seems when I add a domain in kloxo the software only thinks. I get the email it was added, but I check the admin panel and it's not there, sometimes it does create the folder but nothing for the apache domain.
If I add a new domain for the same site, it will make the symlink and over-write the index.html file.
This has happened since I did the upgrade two weeks ago, we got the email fixed and the ssl certs re installed but I need to fix this as I have a client that want's to use their new domain.