I’m posting this just to supply an image to the Unity3d forums of the issue when using refraction shaders with transparent materials. The refraction process in this scene is to mimic underwater FX. However it seems to apply the effect before getting to the transparency Z-buffer part, because I guess transparent objects need to be done last? Anyhow, it causes the transparent objects to ghost, or be shown offset from what they should be as the refraction shifts the objects to a new location but not if it is transparent. This seems to be a common issue with any refraction based shader as I have tried a few and they all do the same thing.
So my solution is to turn off the refraction setting in the underwater system and apply flag style distortion script to the main camera, which gets it looking pretty close to the refraction method but without the transparency ghosting issue.