I'm experiencing a similar problem. Using the Advanced Option to add current categories, the categories are indeed listed as options in the create New Post - type but when selected the new post types don't show up with standard posts that use the same categories.
In fact, I cant' get the new post-type to show up on any webpage unless I select View Post from Edit Page.
For example this link displays candidates created in a standard post whereas this one which was created by the new custom post type.
Interestingly, looking at the new post type on this latter link, at the bottom of the post there are links to the categories that it belongs to but when one clicks on these categories only the standard post types are shown not the new post type!
I'm baffled - Any ideas?