Hi,

I have tested it with a primitive cylinder model, reseted xform and the 2006fbx exporter and the result is the exact same:


If I use Y as up, the models get exported rotated as well (makes sense, since z should be the up axis for me).
Using Z, the models are not rotated neither in MED nor in WED, but they are not spread along the world y axis but are rather positioned along the Z axis of the editor.