/wp-inst/wp-includes/wpmu-functions.php
around line 527
Should this read:
$wpdb->query( "UPDATE $wpdb->sitemeta SET meta_value = '".$wpdb->escape( $value )."' WHERE meta_key = '$key' AND site_id = '$wpdb->siteid'");
rather than
$wpdb->query( "UPDATE $wpdb->sitemeta SET meta_value = '".$wpdb->escape( $value )."' WHERE meta_key = '$key'" );