At the moment it displays the oldest post first in the portfolio section and I want to order by newest post first, but I cant find where to do this I looked in /includes/loop-portfolio.php but cant find where the ordering is set.
Order portfolio with newest post first in Choices2 posts from 2 voices
Please install and activate this plugin http://wordpress.org/extend/plugins/post-types-order/ .. It will let you order your portfolio however you need to.
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