[Plugin: Custom Content Type Manager] advanced content settings: order by

Are you referring to ordering the posts in the manager or on the front end? If the front-end, then it’s up to your template and how it’s using the loop. If in the manager, it’s probably ref’d already by this bug: https://code.google.com/p/wordpress-custom-content-type-manager/issues/detail?id=526 — you can subscribe to updates on the bug tracker to get alerted to when it gets resolved.