Matt,
When I run my model of a storm sewer and ponding system, the pipes do not appear to be increasing flow capacity when operating under a head. In fact, when looking at the time-series plots, the graph peak is cut off at about the design flow capacity. I tried installing a free outfall on several links to see if it was a tailwater condition, but the pipes still did not increase capacity with head. I don't know if I am inputting something wrong or what. I will send my model to you at matt.anderson@autodesk.com and look for your reply.
Thanks for any help you can give,
Bob
Be sure your Hydraulic Routing is set to Hydrodynamic rather than Steady or Kinematic Wave.