Regions not working/disappearing for specific URL

I have a really weird scenario where regions are not showing in admin to edit or outputting on the page if the page location is has a certain folder name/location (courses/acma/index.php). The page is using a master page template that many other pages use without problem. If I change the page location (Eg. courses/acma2/index.php) all of a sudden the regions appear, I can add content and it is output on the page. If I change back, the regions still show up in admin, but they are not output on the page. Any ideas?

The debug from the web page where the regions are not outputting...

Debug Message
[1] SELECT * FROM perch2_pages WHERE pagePath='/courses/acma/index.php' LIMIT 1
[10] SELECT regionKey, regionHTML FROM perch2_content_regions WHERE regionPage='/courses/acma/index.php' OR regionPage='*' ORDER BY regionPage DESC
Using template: /templates/pages/attributes/default.html
Using sub-template: /templates/pages/attributes/seo.html
Using sub-template: /templates/pages/attributes/facebook.html
Using sub-template: /templates/pages/attributes/twitter.html
[67] SELECT * FROM perch2_pages WHERE pageNew=0 AND pageHidden=0 ORDER BY pageTreePosition ASC
[1] SELECT pageTreePosition FROM perch2_pages WHERE pagePath='/courses/acma/index.php' LIMIT 1
[2] SELECT pageID FROM perch2_pages WHERE pageTreePosition IN ('000-002-001', '000-002', '000') ORDER BY pageTreePosition DESC
Using template: /templates/navigation/level1.html
[6] Using template: /templates/navigation/level2.html
[6] Using template: /templates/navigation/level2.html
[6] Using template: /templates/navigation/level2.html
[1] SELECT pageTreePosition FROM perch2_pages WHERE pagePath='/courses/acma/index.php' OR pageSortPath='/courses/acma/index.php' LIMIT 1
[2] SELECT * FROM perch2_pages WHERE pageHidden=0 AND pageNew=0 AND pageTreePosition IN ('000-002-001', '000-002', '000') ORDER BY pageTreePosition
[2] Using template: /templates/navigation/breadcrumbs.html
[1] SELECT pageID, pageParentID, pageDepth, pageTreePosition FROM perch2_pages WHERE pagePath='/courses/acma/index.php' OR pageSortPath='/courses/acma/index.php' LIMIT 1
[4] SELECT * FROM perch2_pages WHERE pageNew=0 AND pageHidden=0 AND pageTreePosition LIKE '000-002-001%' AND pageDepth >=2 AND pageDepth<=3 ORDER BY pageTreePosition ASC
[1] SELECT pageTreePosition FROM perch2_pages WHERE pagePath='/courses/acma/index.php' LIMIT 1
[2] SELECT pageID FROM perch2_pages WHERE pageTreePosition IN ('000-002-001', '000-002', '000') ORDER BY pageTreePosition DESC
[3] Using template: /templates/navigation/item.html
[1] SELECT pageID, pageParentID, pageDepth, pageTreePosition FROM perch2_pages WHERE pagePath='/courses' OR pageSortPath='/courses' LIMIT 1
[7] SELECT * FROM perch2_pages WHERE pageNew=0 AND pageHidden=0 AND pageTreePosition LIKE '000-002%' AND pageDepth >=1 AND pageDepth<=2 ORDER BY pageTreePosition ASC
[1] SELECT pageTreePosition FROM perch2_pages WHERE pagePath='/courses/acma/index.php' LIMIT 1
[2] SELECT pageID FROM perch2_pages WHERE pageTreePosition IN ('000-002-001', '000-002', '000') ORDER BY pageTreePosition DESC
Using template: /templates/navigation/footer_menu.html
[1] Using template: /templates/navigation/item.html
[1] SELECT pageID, pageParentID, pageDepth, pageTreePosition FROM perch2_pages WHERE pagePath='/qualifications' OR pageSortPath='/qualifications' LIMIT 1
[7] SELECT * FROM perch2_pages WHERE pageNew=0 AND pageHidden=0 AND pageTreePosition LIKE '000-003%' AND pageDepth >=1 AND pageDepth<=2 ORDER BY pageTreePosition ASC
[1] SELECT pageTreePosition FROM perch2_pages WHERE pagePath='/courses/acma/index.php' LIMIT 1
[2] SELECT pageID FROM perch2_pages WHERE pageTreePosition IN ('000-002-001', '000-002', '000') ORDER BY pageTreePosition DESC
Using template: /templates/navigation/footer_menu.html
[1] Using template: /templates/navigation/item.html
[1] SELECT pageID, pageParentID, pageDepth, pageTreePosition FROM perch2_pages WHERE pagePath='/information' OR pageSortPath='/information' LIMIT 1
[9] SELECT * FROM perch2_pages WHERE pageNew=0 AND pageHidden=0 AND pageTreePosition LIKE '000-006%' AND pageDepth >=1 AND pageDepth<=2 ORDER BY pageTreePosition ASC
[1] SELECT pageTreePosition FROM perch2_pages WHERE pagePath='/courses/acma/index.php' LIMIT 1
[2] SELECT pageID FROM perch2_pages WHERE pageTreePosition IN ('000-002-001', '000-002', '000') ORDER BY pageTreePosition DESC
Using template: /templates/navigation/footer_menu.html
[1] Using template: /templates/navigation/item.html

Diagnostics:

Perch: 2.8.28, PHP: 5.6.10, MySQL: mysqlnd 5.0.11-dev - 20120503 - $Id: 3c688b6bbc30d36af3ac34fdd4b7b5b787fe5555 $, with PDO
Server OS: Darwin, apache2handler
Installed apps: content (2.8.28), assets (2.8.28), categories (2.8.28), perch_forms (1.8.3)
App runtimes: <?php $apps_list = array( 'content', 'categories', 'perch_forms', );
PERCH_LOGINPATH: /rt_admin
PERCH_PATH: /Users/bradhardinge/Documents/clients/ramsdentraining/site/production/rt_admin
PERCH_CORE: /Users/bradhardinge/Documents/clients/ramsdentraining/site/production/rt_admin/core
PERCH_RESFILEPATH: /Users/bradhardinge/Documents/clients/ramsdentraining/site/production/rt_admin/resources
Image manipulation: GD
PHP limits: Max upload 32M, Max POST 32M, Memory: 128M, Total max file upload: 32M
F1: 2edba60ed1f613d6dd804feb202456a2
Resource folder writeable: Yes
HTTP_HOST: ramsdentraining.dev
DOCUMENT_ROOT: /Users/bradhardinge/Documents/clients/ramsdentraining/site/production
REQUEST_URI: /rt_admin/core/settings/diagnostics/
SCRIPT_NAME: /rt_admin/core/settings/diagnostics/index.php