I never got a response to this, so I had to put a work around in place myself.
Basically what's happening is the Facebook plugin is auto-injecting itself to
the_content - which is fine on single pages, but on a page that is a blog template you end up with all the comments showing up after each post in the loop - it's a cluster.
Ideally it would be nice to either 1) fix this 2) provide a function that can be called in the template to manually place the comments, alas since those are not options at the moment here is what I ended up doing.
In my blog template file I placed:
/** Remove Facebook from auto-injecting comments after each post */
remove_action( 'init', 'fb_apply_filters', 40 );
remove_filter( 'the_content', 'fb_comments_automatic', 30 );
remove_filter( 'comments_array', 'fb_close_wp_comments' );
remove_filter( 'the_posts', 'fb_set_wp_comment_status' );
remove_action( 'wp_enqueue_scripts', 'fb_hide_wp_comments' );
remove_filter( 'comments_number', 'fb_get_comments_count' );
That fixed it.