OK, what about the webassist/plugins/cms_templates/custom_pages.php any changes made to that file?
what are the results if you run this query directly in the database?
SELECT C2.ContentID, C2.ContentGroup, C2.ContentPageSetOrder FROM ps4_contents AS C1 LEFT OUTER JOIN ps4_contents AS C2 ON C2.ContentPagesetParentID = C1.ContentID WHERE C1.ContentGroup = 'Custom Pages' AND C2.ContentPageSetOrder IS NOT NULL GROUP BY C2.ContentPageSetOrder ORDER BY C2.ContentPageSetOrder DESC
can you send a link where i can see the issue.