Aerodynamically, the flaps are working fine. You can't prevent the car from EVER leaving the ground on a spin, other than keeping the flaps open at all times or creating a new design that creates no lift in the first place, which isn't possible. Since you can't do that, you have the flaps we have now: As soon as air hits the car from behind, it also hits the flaps' edge, causing them to deploy. The flaps lift, block airflow over the car, and stop the aerodynamic lift. Car lands.
A NASCAR body might generate downforce while traveling forwards, but the shape inherently creates lift when travelling backwards. This is due to air hitting the car and travelling over and under the car at different speeds, dictated by their shapes - and a NASCAR's shape is generally that of a wing. Airflow over the car is thus faster, and creates low pressures sucking even these 3400 pound behemoths upwards. The only thing possible to prevent that would be blocking airflow over the car, thus restabilizing the pressures between the two sides - this is exactly what the flaps do. The only purely-mechanical way to do it is the current setup: The flaps slightly protrude over the rear window and so, when the air hits the car backwards (such as after a spin), the airflow throws them up - a process that takes about half a second, sometimes slightly more. This delay is inherent to a purely aerodynamically-actuated system. You can shorten that by lengthening the flaps, making the protrude a bit more - at the expense of aerodynamic efficiency when going forwards, and it'll look a bit silly. An electronic system could do that faster, but I don't know how keen NASCAR's governing body would be to have relatively expensive sets of sensors and computers on board to calculate the angle of a spin and such.
I wonder, SolidFro. When you complain about the roof-flaps, do you have any aerodynamic knowledge or understanding to support your claims that they failed to do their duty? Do you even realize that the car started sinking once the flaps deployed, and that Newman's nudge was what launched Carl into the air?