It is possible that the objects that are not showing up in iRhino 3D do not yet have render meshes. To test this theory: in Rhino-proper, run the
Shade command with all objects you want to see in iRhino 3D visible (layers on, not hidden). This will add the render meshes to all the visible geometry. Save the file (but don't use Save Small; this deletes the render meshes) and try loading it in iRhino 3D again. Does this help?