I have not that usual bug like water aint showing up. My water is working and I can see it. No leaks or that kind of stuff.
Only problem is, at some points my water reflection get stuck. eg. I walk near my water and the reflection is fine, but at some moment the reflection get stucked and moves with me and stops reflection.
Hope its clear enough, will post some screenshots later.
Each water need it's own Env_CubeMap. Place one above each brush of water and open it's properties. Click "Brush Faces" and select the top face of the water. You should get a line between the Env_CubeMap and the water in the 3D view. Compile and enter the game. When playing the map, type into the console "buildcubemaps". This will then take pictures in all six directions around each Env_CubeMap for use with reflections. You need to reload the map (or possibly the game) to see the result.