Tom

I’m experiencing the same issue.

I am working on two different sites, both running WordPress v3.5.2 and Yoast SEO v1.4.13.

On one site the Twitter Cards meta tags are appearing as expected – on the homepage and individual posts.

On another the meta tags are only appearing on individual posts and not on the homepage…

You may have already figured out a solution, but what you could do is:

Assign the categories you want to the posts which are in the Uncategorized category using the Bulk Actions feature. If you have a lot of posts, you can increase the number shown on each page by adding something like this to your theme’s functions.php file:

function my_edit_posts_per_page($posts_per_page) {
   return 200; // Change this to the number of posts per page you want.
}
add_filter('edit_posts_per_page', 'my_edit_posts_per_page');

Next, change the Default Post Category in Settings >> Writing to something other than Uncategorized.

Now you should be able to delete the Uncategorized category.