Put QoS on main gateway and see if there are any bottlenecks anywhere else in the network. Keep us informed of what has worked for you. And I can suggest these materials for reading: http://forum.mikrotik.com/t/help-please-on-shaping/25634/4 http://forum.mikrotik.com/t/tree-queues-and-traffic-priority/25135/3
http://forum.mikrotik.com/viewtopic.php?f=13&t=29211&start=0