One more notification something I noticed, it only happens in shortcodes that are used on Custom Posts. It doesn’t happen to the shortcodes that are placed on normal pages.

So to summarize what I found out:

The navigation dissapears on the captures page once the masonry=”1″ is removed from the shortcode. The post_count does not make a difference.

The captures however is a custom post “gallery”

While the same shortcode with the masonry added on the pictures page does not show a navigation.

I am fairly certain by now that the issue somehow lies with the custom posts not using the setting from intense to remove the nav.