The display order for issues, whether that be in the archive issues screens in the flipbook and mobile interfaces, OR on the custom publishing domain landing page, is dependent on the publish date (pub date).  Issues are displayed latest to earliest.

To change the pub date, go to your manage titles/issues view and click on the pencil on the right of the "Pub date" field.

Change the date to get that particular issue in order.   You may have to do this when you are uploading archive/older issues as they automatically are assigned a pub date of the time of upload.