Drag/Heat Shield not redrestrating

My current build is a ship inspired by a book call StarShip Troopers(really good book incase you have never read it). In the book the troopers begin their attack on a planet in a 1-man capsule in orbit around the planet. As they decend the ships heat shield burns off in distinct layers- 1, 2 and 3. Because the ship is circular I used fairings. The first layer works fine with the heat shield burning off and the ship losing speed. The heat shield depleted I activate the next stage. The fairing nose cones jettison and another fresh layer is exposed. Here is where the bug starts. The second and third layers take about 1 minute(not sure exactly) to regristrait drag and heat. By the time they start regristrating drag and losing heat shield I am at about 1000m above sea-level and doing 2500m/s(for Droo).