The most likely reason for this happening is misconfiguration of policies and/or partitions.
To troubleshoot this problem, turn shaping off. If the slow-down goes away, PacketWise is not optimally configured for the traffic patterns on your network. You should study your policies and partitions and look for obvious problems. You can also try removing policies and partitions one at a time, turn shaping on, and see if this single change improves network performance. This process will help you determine which policy/partition is configured incorrectly. If you turned shaping off and network performance is still slow, the problem lies somewhere else. PacketWise is still classifying traffic, even with shaping off, so an abundance of flows (for example, from a denial-of-service attack) could be slowing network traffic down. For more information about DoS attacks, see KB2029