It actually has to do with the system being set up to read centers of objects, not their actual bounding area. So if you rez a prim floor of 20 x 10 x 1.0, then rez a prim on top of it, the prim sinks down into it based on the Z parameters for both prims. And if the rotation of the floor prim is facing downward it will attempt to rez the object on top of it, which of course is underneath it. This is because instead of calculating the area a prim really has, the system is only getting it's centerpoint and rotations. Something on our big list of overhauls to get worked on
