For joomla sites i use this Apache Directive and they works ok.
Code:
<Directory /var/www/webxx/web/>
Options +Includes +FollowSymlinks -Indexes
AllowOverride All
Order allow,deny
Allow from all
<Files ~ "^\.ht">
Deny from all
</Files>
</Directory>
Your enviroment works ok and now you have this problem? Or this problem is after ISPConfig installation?