Apologies in advance for asking what may be a stupid question but does WPMU by default ping Ping-O-Matic with each new post for everyone's blog? I notice in execute-pings.php that this line execute_all_pings(); is commented out.
On a possibly related note register_shutdown_function('do_trackbacks', $post_ID); is commented out in wp-includes/functions-post.php does this mean trackbacks are not being done?