It works fine for me in flare studio anf also in f3D files exported from Studio Max. Just don't forget to set a higher layer for object with transparency texture to calculate the alpha after the object without alpha.
And there is my code :
public function Test()
{
scene3D = new Viewer3D(this);
scene3D.registerClass( Flare3DLoader1 );
scene3D.addChildFromFile("testFrom3ds.f3d");
scene3D.addEventListener(Scene3D.COMPLETE_EVENT, onComplete);
}
private function onComplete(e:Event):void
{
scene3D.getChildByName("Plane001").setLayer(1);
}