I am using your version of the water shader. It is still happening. As soon as I reach a level with the water shader the games performance completely dies - even after loading levels without the shader.

Level 3 - i get 60fps when I load the game on that level.
Level 2 - i get 20fps because of the water shader.
When I load level 2 and pass to level 3, level 3 runs at 20fps.