I created a project with custom type, with only my custom module turned on and no other modules (not even the portal module). When I use the left navigation menu to navigate to the project, it leads me directly to my preset custom module. This is the correct expected behavior. However, if I put in a "projects" web part in the home portal, the links to the projects direct me to an empty "portal" page for the project instead of the module. I suspect this is a bug.