bmap waterbump = <waves2.tga>;
bmap envspec = <sky.tga>;

function mtl_ffpwater_event();

material mtl_ffpwater
 {
   skin1=waterbump;
   skin2=envspec;

   event = mtl_ffpwater_event;
   effect = "water.fx";
}

function mtl_ffpwater_event()
{
	while(1)
	{
		//Lets make it scroll in some direction
		mtl_ffpwater.skill1 += 0.1*time_step;	//Move the water along the x axis with the given speed
		mtl_ffpwater.skill2 += 0.1*time_step; //Move the water along the y axis with the given speed
		mtl_ffpwater.matrix31 = floatd(sin(mtl_ffpwater.skill1)*100000,40000);
		mtl_ffpwater.matrix32 = floatd(cos(mtl_ffpwater.skill2)*100000,40000);
		wait(1);
	}
}

action Water
{
	mtl_ffpwater.matrix11 = float(100); //Tilefactor of the Bumpmap in x direction
	mtl_ffpwater.matrix22 = float(100); //Tilefactor of the Bumpmap in y direction

	bmap_to_mipmap(mtl_ffpwater.skin1);
	bmap_to_mipmap(mtl_ffpwater.skin2);

	my.material = mtl_ffpwater;
}

Quote:

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what causes those black areas?

I took this screen from your published game in the downlad

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Sorry, I have no idea-.-
It looks alright here. Which graficscard do you have?
If anyone else has this problem, please tell me