The graph is not part of the *.blend file where you store your scene. You must save it manually to an extra file. So be careful: If you only store the scene with Blender save commando the graph is lost. This limitation comes from my understanding of Blender. My be there is an better solution in one of the next releases of this plug in. The advantage of this implementation is that you can use the Save and Load buttons to export a graphs an reload it in an other 3D scene.

In folder "samples" you can find some predefined graphs. You can load them with InnerWorld and then press Mesh to generate the mesh.