I'm not sure about this at all, but try this theory out. The flow down the side of the car is probably better, but the flow underneath the car has been inhibited. Flow under the car may have normally ejected at the rear wheel well but is now getting caught parachute-style. I'm guessing here, but it you added rear wheel spats and perhaps a front air dam, the parachute effect would disappear and you'd see a net gain.
Having no experience with the skirts yet
you probably want somebody else with some expertise to chime in.