The main problem was that the default Atlantis only simulates subsonic aerodynamics. At supersonic speeds, it produces too much lift and too little drag.
There is an important quality called maximum lift-to-drag (L/D) to judge the performance of aerodynamic vehicles: At subsonic speeds, like during landing, the Shuttle has a L/D of 4.5 (which is a flying brick with style). At supersonic speeds, high in the atmosphere at high speed, the L/D is only about 1.0-1.6 (Which is much more like a flying brick). That's an important difference, since L/D for example determines how far something glides for every drop in altitude. The default Atlantis would be constantly overshooting unless you plan some extra miles in your re-entry - it needs 3-4.5 times more distance to glide home at constant speed (but the distance is a bit shorter since the Shuttle slows down during a slightly more shallow glide).
In SSU, this all went a little further and more out of control...