Custom post type not sorted when using custom menu with custom taxonomy

First off, let me say I love the plugin! It works great for me re-organizing a custom post type when I display that post type’s archive page.

However, if I use the wordpress custom menu to link to a taxonomy term from a custom taxonomy, those posts display with their published date order, not the re-arranged order.

Any idea of a fix for this?

Again, thanks for the work on this.

http://wordpress.org/extend/plugins/intuitive-custom-post-order/