I have the same problem.
I've installed a wordpress on one website and a pydio on another website. As soon as I enable the Pydio site, the wordpress domain points to the pydio instead.
It's done two days ago so there was enough time for DNS propagation timeout to be passing.

I've tried it with several wordpress websites too. Strange thing is most of the times it shows the correct websites but sometimes default website which is very annoying.

I wonder if any one can give me some help?
Here is my /etc/ajenti/vh.json file:

---

{
"websites": [
{


"maintenance_mode": false,
"locations": [
{
"custom_conf_override": false,
"path_append_pattern": false,
"pattern": "[^/]\\.php(/|$)",
"custom_conf": "# Zero-day exploit defense.\n# http://forum.nginx.org/read.php?2,88845,page=3\n# Won't work properly (404 error) if the file is not stored on this server, which is entirely possible with php-fpm/php-fcgi.\n# Comment the 'try_files' line out if you set up php-fpm/php-fcgi on another machine. And then cross your fingers that you won't get hacked.\ntry_files $uri =404;\nfastcgi_split_path_info ^(.+\\.php)(/.+)$;",
"path": "",
"match": "regex",
"backend": {
"params": {
"php_admin_values": "open_basedir = none;",
"php_flags": "",
"pm": "dynamic"
},
"type": "php-fcgi"
}
}
],
"custom_conf": "",
"ssl_key_path": "/etc/ssl/pydio_key.pem",
"owner": "root",
"ssl_cert_path": "/etc/ssl/pydio_cert.pem",
"custom_conf_toplevel": "",
"name": "pydio",
"enabled": false,
"extensions": {
"ajenti.plugins.vh.processes.ProcessesExtension": {
"processes": []
},
"ajenti.plugins.vh-vsftpd.vsftpd.VSFTPDExtension": {
"username": "pydio",
"password": "Something",
"user": null,
"created": true
},
"ajenti.plugins.vh-mysql.mysql.MySQLExtension": {
"users": [
{
"password": "Something",
"name": "pydio"
}
],
"databases": [
{
"name": "DB2"
}
]
}
},
"domains": [
{
"domain": "DOMAIN 2"
}
],
"root": "/srv/pydio",
"ports": [
{
"spdy": false,
"ssl": false,
"host": "*",
"port": 80,
"default": false
},
{
"spdy": false,
"ssl": true,
"host": "*",
"port": 443,
"default": false
}
]
},
{
"maintenance_mode": false,
"locations": [
{
"custom_conf_override": false,
"path_append_pattern": false,
"pattern": "[^/]\\.php(/|$)",
"custom_conf": "# Zero-day exploit defense.\n# http://forum.nginx.org/read.php?2,88845,page=3\n# Won't work properly (404 error) if the file is not stored on this server, which is entirely possible with php-fpm/php-fcgi.\n# Comment the 'try_files' line out if you set up php-fpm/php-fcgi on another machine. And then cross your fingers that you won't get hacked.\ntry_files $uri =404;\nfastcgi_split_path_info ^(.+\\.php)(/.+)$;",
"path": "",
"match": "regex",
"backend": {
"params": {
"pm": "dynamic",
"php_admin_values": "open_basedir = none;",
"php_flags": ""
},
"type": "php-fcgi"
}
}
],
"custom_conf": "# Allow file upload to 100MB.\n# Default size is 2MB which is very small for most of images and files.\nclient_max_body_size 100M;\n\n# This order might seem weird - this is attempted to match last if rules below fail.\nlocation / {\n\ttry_files $uri $uri/ /index.php?$args;\n}\n\n# Add trailing slash to */wp-admin requests.\nrewrite /wp-admin$ $scheme://$host$uri/ permanent;\n\n# Directives to send expires headers and turn off 404 error logging.\nlocation ~* ^.+\\.(ogg|ogv|svg|svgz|eot|otf|woff|mp4|ttf|rss|atom|jpg|jpeg|gif|png|ico|zip|tgz|gz|rar|bz2|doc|xls|exe|ppt|tar|mid|midi|wav|bmp|rtf)$ {\n access_log off; log_not_found off; expires max;\n}\n\nlocation = /favicon.ico {\n\tlog_not_found off;\n\taccess_log off;\n}\nlocation = /robots.txt {\n\tallow all;\n\tlog_not_found off;\n\taccess_log off;\n}\n\n# Deny all attempts to access hidden files such as .htaccess, .htpasswd, .DS_Store (Mac).\n# Keep logging the requests to parse later (or to pass to firewall utilities such as fail2ban)\nlocation ~ /\\. {\n\tdeny all;\n}\n# Deny access to any files with a .php extension in the uploads directory\n# Works in sub-directory installs and also in multisite network\n# Keep logging the requests to parse later (or to pass to firewall utilities such as fail2ban)\nlocation ~* /(?:uploads|files)/.*\\.php$ {\n\tdeny all;\n}",
"ssl_key_path": "/etc/ssl/Domain1_key.pem",
"owner": "root",
"ssl_cert_path": "/etc/ssl/Domain1_cert.pem",
"custom_conf_toplevel": "",
"name": "DOMAIN 1",
"enabled": true,
"extensions": {
"ajenti.plugins.vh.processes.ProcessesExtension": {
"processes": []
},
"ajenti.plugins.vh-vsftpd.vsftpd.VSFTPDExtension": {
"username": "username1",
"password": "Something",
"user": null,
"created": true
},
"ajenti.plugins.vh-mysql.mysql.MySQLExtension": {
"users": [
{
"password": "Something",
"name": "username1"
}
],
"databases": [
{
"name": "DB1"
}
]
}
},
"domains": [
{
"domain": "DOMAIN 1"
}
],
"root": "/srv/Domain1",
"ports": [
{
"spdy": false,
"ssl": false,
"host": "*",
"port": 80,
"default": false
},
{
"spdy": false,
"ssl": true,
"host": "*",
"port": 443,
"default": false
}
]
}
]
}