Karen over at BlazingMinds ran into some issues with WordPress 2.9 that since the upgrade pings and tracebacks stopped working. A simple tweak to her cron.php solved the issue, the parameter that was changed is related to the timeout, so I assume the 1 ms timeout isn’t sufficient time to acquire or transmit a pingback in most cases.
Simply look for cron_url line and change 0.01 to 1 should resolve the issue if you are having similar problems.
$cron_url = get_option( â€™siteurlâ€™ ) . â€˜/wp-cron.php?doing_wp_cronâ€™;
wp_remote_post( $cron_url, array(â€˜timeoutâ€™ => 0.01, â€˜blockingâ€™ => false, â€™sslverifyâ€™ => apply_filters(â€˜https_local_ssl_verifyâ€™, true)) );
Though I didn’t notice this issue myself, go read the post over at BlazingMinds and determine if you have the same issue and if this fix resolves yours as well.