Custom post types in custom menus

I recently created a site which had Custom Post Types. I used the 3.0 Custom Menus to create various menus on the site. When installed, the Menus panel on the admin dashboard displayed boxes to be able to add in the custom posts type posts into any menu. This was brilliant and exactly what I needed.

However, these have now disappeared without changing any code. Has any one else come across this?

Huw