Unfortunately my happiness was a little too early, apparantly it wasn’t adding the post count that did the trick but removing the masonry from the shortcode.
Now on another page where I need the masonry in the shortcode I have the same problem again.
Even with post count set I get the prev and next navigation below my custom post shortcodes.
Also another thing I noticed, is although on the blog settings the prev next nav is turned off on my custom posts it still shows also on the individual posts so not just below the shortcodes.
For some reason the custom posts do not abide by the settings.
Hope you can look into this for me.