I have the same problem. I created a course format and the "Add an Activity or Resource" link is inactive. If I switch to the "Topics" format it is active again. As you can see in the capture below the link is black, not blue, indicating it is just plan text. I have viewed the html source for both formats and it is the same for each:
<div class="hd choosertitle">Add an activity or resource</div>This is a div that gets a link action added by yum at some point. When the page first appears in the topics page is is also text, but eventually turns into a link. I suspect that the yum assignment is failing for the custom course formats.