Ian,
Bill James has a very nice SWMM Conceptual Workbook that talks about sensitivity analysis and the response of the model to changes in various parameters on an urban catchment. Essentially, small storms are influenced most by PCTZER and % imperviousness. For large storms, changes in slope, width, % imperviousness., maximum infiltration, and minimum infiltration are the key parameters.
Given your situation, I'd suggest examining the following:
1. Try lowering PCTZER and %imperviousness to get a better match on the small storms.
2. If possible, reanalyze the rainfall data to obtain 15 minute or small time increments. This should improve the response of the model to the actual conditions.
Roger W. Lehman, P.E.
Lehmanr@mail.rfweston.com