For this to work, you cannot have both a "Cheap" and "Expensive" versions of water in the save view. Also, the water levels must be at the same height. Also, only the top surface of the brush must be water, the others must be NoDraw. Make sure you use a proper water texture, avoiding any with "_beneath" or "_underside", etc, on the name. Place a Cubemap 64 units above the water surface and attach it to the water's face. Buildcubemaps.
I was hoping to answer a few of the above with the texture names.
Check those, then come back. If you still have issues, I may need to see the VMF myself.