I have made a world with Water4 and custom skybox. Water4 reflects the current custom skybox just as it should, but I can still see white reflection of the basic sun (the white ball) on the water surface, even when it’s not part of the skybox or the scene (I can’t be sure about this of course since I’m a new user, but I at least can’t find it in the scene).
You have to bake the lighting in your scene. Click on Window>Lighting. A Lighting window will open. In here setup your ‘Skybox’ to the one you are using and in the ‘Sun’ select the main source of light in your scene. Than scroll down, untick ‘Auto’ or ‘AutoGenerate’ and click on ‘Build’ or ‘Generate Lighting’.