The runway configuration management (RCM) problem governs what combinations of airport runways are in use at a given time, and to what capacity. Runway configurations (groupings of runways) operate under runway configuration capacity envelopes (RCCEs) which limit arrival and departure capacities. The RCCE identifies unique capacity constraints based on which tarmacs are used for arrivals, departures, or both, and their direction of travel. When switching between RCCEs, some decrement in arrival and departure capacities is incurred by the transition. A previous RCM model (Frankovich et al., 2009) accounted for this cost through a required period of inactivity. In this paper, we instead focus on the introduction and assessment of a model capable of marginally decreasing RCCE capacities during configuration transitions. A transition penalty matrix is introduced, specifying the relative costs (in terms of accepted arrival and departure capacities) for switching between RCCEs. The new model benefits from customizable transition penalties which more closely represent real-world conditions, at a reasonable computational cost.