Error in Perch after upgrading

Hi,

I have recently updated PHP and other things on a client's server as well as their version of Perch and now I am receiving the following error when trying to pass variables into a template. They have other sites (exact same code but themed) on the same server using an old version of Perch and these are working correctly still, so the problem seems version related.

The error is

Debug Message
[4] SELECT regionKey, regionHTML FROM perch2_content_regions WHERE regionPage='/apply.php' OR regionPage='*' ORDER BY regionPage DESC
[nil] SELECT regionID, regionTemplate, regionPage, regionRev AS rev FROM perch2_content_regions WHERE regionKey='Application Form' AND (regionPage='/apply.php' OR regionPage='*')
No matching content regions found. Check region name (Application Form) and page path options.
[nil] SELECT * FROM ( SELECT idx.itemID, c.regionID, idx.pageID, c.itemJSON, idx2.indexValue as sortval FROM perch2_content_index idx JOIN perch2_content_items c ON idx.itemID=c.itemID AND idx.itemRev=c.itemRev AND idx.regionID=c.regionID JOIN perch2_content_index idx2 ON idx.itemID=idx2.itemID AND idx.itemRev=idx2.itemRev AND idx2.indexKey='_order' WHERE idx.regionID IS NULL AND idx.itemID=idx2.itemID AND idx.itemRev=idx2.itemRev ) as tbl GROUP BY itemID, pageID, itemJSON, sortval ORDER BY sortval ASC
Using template: /templates/content/application_form.html

and the offending region in the template looks like

<?php     
    PerchSystem::set_var('activeJob', $_GET['job']);
    PerchSystem::set_var('location', $_GET['subregion']);

    perch_content_custom('Application Form', array(
        'template'=>'application_form.html'
    ));    
?>

I've checked in the DB using the following SQL

SELECT * 
FROM  `perch2_content_regions` 
WHERE regionPage =  "/apply.php"

and the content region is there with what looks like the appropriate HTML.

Finally my diagnostics

HEALTH CHECK

Perch is up to date
PHP 5.5.9-1ubuntu4.14 is up to date
MySQL 5.5.47-0ubuntu0.14.04.1 is up to date
Image processing available
SUMMARY INFORMATION

Perch: 2.8.29, PHP: 5.5.9-1ubuntu4.14, MySQL: 5.5.47, with PDO
Server OS: Linux, apache2handler
Installed apps: content (2.8.29), assets (2.8.29), categories (2.8.29), perch_forms (1.8.3)
App runtimes: <?php $apps_list = array( 'content', 'categories', 'perch_forms', );
PERCH_LOGINPATH: /perch
PERCH_PATH: /var/www/<mysite>/perch
PERCH_CORE: /var/www/<mysite>/perch/core
PERCH_RESFILEPATH: /var/www/<mysite>/perch/resources
Image manipulation: GD
PHP limits: Max upload 20M, Max POST 8M, Memory: 128M, Total max file upload: 8M
F1: 2edba60ed1f613d6dd804feb202456a2
Resource folder writeable: Yes
HTTP_HOST: <mysite>.co.uk
DOCUMENT_ROOT: /var/www/<mysite>
REQUEST_URI: /perch/core/settings/diagnostics/
SCRIPT_NAME: /perch/core/settings/diagnostics/index.php

Many thanks

Lee