The Box (EX9 Geometry) Node can only create one type of box at a time, whereas the Box (ODE) is spreadable. This makes it uncomfortable when using many different sized Boxes in an ODE Environment.
Might be the same with Spheres.
to spread EX9 geos is to spread its transformations, this even works for ODE geos. if wont care about, you can try tonfilm-ODEGeosAndTransform