Thank you for the suggestions Susan,
in my .htaccess file I added
RewriteEngine On
RewriteBase /pgh3/
The template file had comments about Apache mod_rewrite so I enabled this with
and restarted Apache.
I have double checked the config.inc.php file, config.core.php files and config.inc.php file by comparing them line by line with a working installation in another subdirectory
config.inc.php
$modx_core_path= '/var/www/html/pgh3/core/';
$modx_processors_path= '/var/www/html/pgh3/core/model/modx/processors/';
$modx_connectors_path= '/var/www/html/pgh3/connectors/';
$modx_connectors_url= '/pgh3/connectors/';
$modx_manager_path= '/var/www/html/pgh3/manager/';
$modx_manager_url= '/pgh3/manager/';
$modx_base_path= '/var/www/html/pgh3/';
$modx_base_url= '/pgh3/';
$modx_assets_path= '/var/www/html/pgh3/assets/';
$modx_assets_url= '/pgh3/assets/';
config.core.php
define('MODX_CORE_PATH', dirname(__FILE__) . '/core/');
define('MODX_CONFIG_KEY', 'config');
/connectors/config.core.php
define('MODX_CORE_PATH', dirname(dirname(__FILE__)) . '/core/');
define('MODX_CONFIG_KEY', 'config');
/manager/config.core.php
define('MODX_CORE_PATH', dirname(dirname(__FILE__)) . '/core/');
define('MODX_CONFIG_KEY', 'config');
Manually cleared the cache directory, and browser cache multiple times, logged out and logged in again, tried a different browser etc
Still the same problem though, nothing has changed.