Just got a server with Debian/ISPConfig 3, migrated a couple websites without any problem but now I'm having problems with one particular website. The difference with the others is the directory structure since this one uses some directories outside of "web" to improve the database connections security. It seems it can't figure the path to the files inside "Connections".
Maybe it doesn't like the symlinks, try using the full path eg: /var/www/clients/clientX/webX/Connections PS: If it's php you might need an open_basedir or a php_value include_path statement.
