Yeah, that part I get. I was just hoping my occasionally-used FX would shut themselves off when I changed Scenes (or re-selected the active Scene). No way to do that? Not sure I'm saying this right...
They will once you've saved the state of a given scene with that effect off. The default is for each scene to have each effect enabled, so unfortunately if you add an effect that you only want on in one scene, you have to go to each scene and turn it off, save, then repeat for the next scene.
Make sure you save the patch every time you want to save a scene's config, before moving on to the next scene. Myself, I wish the default was for a newly added block to be in its off state, but oh well.
For example, I want a phaser in scene 3, and only scene 3. I plop a phaser block in the grid. Then I go to scene 1, disable the phaser, save the patch. Then I do the same for scenes 2, 4 and 5. Now, if hit scene 3, play for a bit, click the phaser IA to turn the phaser off, play, then hit scene 3 again - the scene WILL revert back to its saved state, and the phaser will be turned back on. Or the inverse example: I'm in scene 1, I click the phaser on for a bit - I can hit scene 1 again and the phaser will be turned off (or any other scene that that phaser is off, i.e. scenes 2,4,5).