The 2nd qual lap is way slower on all the tracks with high tire wear, that includes Atlanta, Fontana, Chicagoland, Darlington, Kansas, Las Vegas, Lowe's, The Rock, Texas (if you run both laps hard instead of cruising around first lap 3 seconds off pace in order to have a better speed and still fresh tires going into lap 2).

As you said, the 2nd lap is always way faster on SS, and both laps are about equal (within a tenth) on all the other standard tracks (not sure about Indy / Pocono where you always blow up on lap 2 anyway, though).