Custom post type updated to support comments, yet comments don’t appear

You can use a function called add_post_type_support

Hook into init after the post types have been created, and add support for comments.

add_action('init', 'my_cpt_add_excerpt', 100);
function my_cpt_add_excerpt() {
    add_post_type_support('mycpt', 'excerpt');
}

…where mycpt is the name of your custom post type.

If you want to do it cleanly, you can always deregister the custom post type, and then register it again with the corrected supports array.

Further reading: http://codex.wordpress.org/Function_Reference/add_post_type_support