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.