Hi guys !
First of all, thanks again for this plugin, it is helping me a great deal.
I have the same issue as frizky.
I deactivated every plugins except for MB and MB Custom Post Type.
I don't know if this is a clue but there is absolutely no issue when my new post type is set to page or post: it is well displayed in the navigation and wherever I want, using "Show as top-level menu" or any other choices "sub-menu of ...".
This only happened with Capability type set to custom.
I investigated a few topics here in order to resolve my issue, but nothing seems to work.
Hope you find a solution for this matter !