if you use Custom top level configuration, or define server_name manualy, this why you get thats error
check your /etc/nginx/conf.d/yoursite.conf
for two server block , and two server_name
if there is two of them, delete the one your dont want

Hey Joe Tuley
first of all, what r u trying to do? and whats your OS?
you should install ajenti on fresh install OS , and update all of your package,
i guess you use centos 6, and wan install ajenti
i think you use centos 6 , earlier used , not fresh install , that's why you getting error
update your system with {yum update} and try again install ajenti, if doesn't work and getting error again
do these steps ,maybe your problem will solved
clean your yum meta , and update & upgrade yum, then install latest ajenti rpm , as following

yum clean metadata
yum upgrade
yum update
yum install rpm
rpm -ivh http://download.fedoraproject.org/pub/epel/6/x86_64/epel-release-6-8.noarch.rpm
rpm -ivh http://repo.ajenti.org/ajenti-repo-1.0-1.noarch.rpm
yum install ajenti -y
systemctl restart ajenti
systemctl stop firewall

sorry for my bad engish, be happy

first of all you should remove mariadb, becaz ajenti dosnt support maria db
then you shoud install mysql-server
you cant use yum install mysql , becaz no longer centos support MySQL, and install mariadb instaed
you shoud install mysql-server like this

yum instal mysql-server

then config mysql

sudo /usr/bin/mysql_secure_installation

when you run this code , ask you couple question abour securing mysql, you shoud config root user and set password

install and enable mysql

sudo yum install mysql-server 
sudo service mysqld start

go to ajenti , select mysql from software section ,and enter your data like this
host: 127.0.0.1 or localhost
username: root
password: your password

restart ajenti , and done

sorry for my bad english, be happy

use bind plugin,
i explain on centos 7
first step: install bind

yum install bind
or
yum install bind9

then configure your nameservers from custom name server section in ajenti
restart ajenti
in the software section , will add new item named, bind9
click on it, and configure it like this

this is sample bind configure for my domain,
my main domain is lexyco.net
and my host name is ms.lexyco.net
and my name servers is ns.lexyco.net & ns1.lexyco.net & ns2.lexyco.net
i have one main ip 92.222.136.102

i hope you get it ,
sorry for my bad english, be happy


$TTL 604800
@ IN SOA ns.lexyco.net. ms.lexyco.net. (
1 ; Serial
604800 ; Refresh
86400 ; Retry
2419200 ; Expire
604800 ) ; Negative Cache TTL
;
; name servers - NS records
IN NS ns.lexyco.net.
IN NS ns1.lexyco.net.
IN NS ns2.lexyco.net.
s1 IN NS ns28.serverpars.com.
s1 IN NS ns29.serverpars.com.

; name servers - A records
ns IN A 92.222.136.102
ns1 IN A 92.222.136.102
ns2 IN A 92.222.136.102

; main - A records
@ IN A 92.222.136.102
lexyco.net. IN A 92.222.136.102
* IN A 92.222.136.102
mx IN A 92.222.136.102
imap IN A 92.222.136.102
smtp IN A 92.222.136.102

; subdomain - A records
pma IN A 92.222.136.102

; cname records
www IN CNAME lexyco.net.

lexyco.net IN AAAA ::1

in the nginx configuration of your site >> content tab >> custom confiquration
enter youre server_name like this
server_name yourdomain.com *.yourdomain.com;

im looking for this capability too,
you shoud ask developers to add this capability to ajenti
there is nothing we can do, becaz ajenti will overwriting the configuration
if you r progamer,and familiar with python, get involved and do it your self

packages section for updating packages or search the packages
if you have no entries wich means , all your packages is up to date , and you don't need any update
ajenti dont list packages , just show package needed update

you can use , other package for your os,like fail2ban

in cent os , you shoud disable your firewalld and iptables

then enter your admin addres with https like this
https://yourdomain:8000

yeah , i like your idea so much