Lol, I guess I should close this now.
I finally realised it was just something to do with the shader I was using (I downloaded from EVOLUTION, 2 water shaders) I tried using the less advanced one first and it didn't work. This put me off using the other one but then today, I did, and it works fine. So yeh, my water in my game is good now, and there is no point in this thread anymore.
(Here's an image of my resultant water shading:
)
Cowbox
Soharix HQ
http://www.soharix.homestead.com/
P.S. Thanks for everyones help anyway.