Are you sure there is nothing wrong with your settings while rendering?
Check if the glass and the water geometry interfere. Post the 3dm file to check it

try reducing the size of the water very slightly so is is not in the exact same place as the glass but just inside it.

That's the thing.. if you offset the water surface in a slight amount, the material won't bleed through in the rendering. You could also give the top surface of the water a little shape to simulate the affect of surface tension on water being held in a glass container.