Check your router and LAN switch/hub NIC speeds. If they auto-negotiate and PacketShaper/AppVantage also is auto-negotiating the link speed, you could have issues due to packet loss. Packet loss robs your network of its efficiency because it has to retransmit packets.
A common mis-negotiation problem we have seen occurs when the router is running at 10 Mbit/sec half duplex and the LAN switch/hub is running at 100 Mb/sec full duplex. The result is often a slow-down. Find the common link speed that works as the least common denominator and set all NIC cards to that speed. In this example, it would be 10 Mbit/sec half-duplex. Set the LAN switch/hub to 10 Mbit/sec half duplex and also set both NICs on PacketShaper/AppVantage. Some models support this setting -- for example, the PacketShaper 4500.For information on analyzing network performance, see PacketGuide Recommendations, for example Identify Performance Saboteurs.