If what you are trying is to change the time multiplier for all the effects in your scene, this should be easy to do with a simple Unity script by just getting the "PKFxRenderingPlugin" component from your camera and access the "m_TimeMultiplier" public variable:
GameObject camera = GameObject.Find("PKFxCamera");
camera.GetComponent<PKFxRenderingPlugin>().m_TimeMultiplier = 2.0f;
And you also have a slider in the Unity editor if you check the "Show Advanced Settings" option on your camera, so you can see this slider changing at runtime if you modify it from a script:
But I guess that's what you are already doing.
If you are trying to change the time multiplier per effect, there is currently no way of doing that.
Concerning the bug you are experiencing, could you describe it with a little bit more details? What do you mean by "everything has to be re-hooked up again"?
Also if you think this bug could be caused by a recent plugin update, you can try the "safe way" to update:
Hope this helps