In the action 'nice_waves' I have set my.transparent=off; that did the trick.
But I like the water transparent so I commented out the parts that I don't need in the wdl file generated by IceX;

Code:

---

/////////////////////////////////////////////
//Script generated by IceX 2.0 Editor////////
/////////////////////////////////////////////

//bitmaps
bmap detail_texture1=<icx_detail1.tga>;
bmap detail_texture2=<icx_detail2.tga>;
bmap detail_texture3=<icx_detail3.tga>;
bmap detail_texture4=<icx_detail4.tga>;
 
//variables
var d3d_autotransparency = on;
var d3d_mipmapping = 0;
 
////defines
//define _alpha_sort, flag1;
 
//functions
function mtl_terrain_multitex_init();
//function mtl_entity_alpha_init();
 
//material for terrain
material mtl_terrain_multitex
{
	skin1 = detail_texture1;
	skin2 = detail_texture2;
	skin3 = detail_texture3;
	skin4 = detail_texture4;
 
	event = mtl_terrain_multitex_init;
}
 
////material for entities
//material mtl_entity_default
//{
//	emissive_blue  = 0;
//	emissive_red   = 0;
//	emissive_green = 0;
//	ambient_blue  = 150;
//	ambient_red   = 150;
//	ambient_green = 150;
//	specular_blue  = 0;
//	specular_red   = 0;
//	specular_green = 0;
//	power = 1;
//	albedo = 15;
//}
 
////material for entities with tga skin
//material mtl_entity_alpha
//{
//	emissive_blue  = 0;
//	emissive_red   = 0;
//	emissive_green = 0;
//	ambient_blue  = 150;	
//	ambient_red   = 150;
//	ambient_green = 150;
//	specular_blue  = 0;
//	specular_red   = 0;
//	specular_green = 0;
//	power = 1;
//	albedo = 15;
//	
//	event=mtl_entity_alpha_init;
//	effect
//	"
//	texture entSkin1;
//	dword mtlSkill1;
//	
//	technique t1
//	{
//		pass p0
//		{
//			Texture[0]=<entSkin1>;
//			ZWriteEnable=True;
//			AlphaBlendEnable=False;
//			AlphaTestEnable=True;
//			AlphaRef=<mtlSkill1>;
//			AlphaFunc=Greater;
//			CullMode=CCW;
//			ColorArg1[0]=Texture;
//			ColorOp[0]=Modulate2X;
//			ColorArg2[0]=Diffuse;
//		}
//	}
//	";
//}
 
//initialising level
starter init_level
{
	level_load("first_level.wmb");
	
	wait(2);
	
	fog_color = 1;
	
	camera.fog_start = 100;
	camera.fog_end = 30000;
	camera.clip_near = 5;
	camera.clip_far = 45000;
	
	effect_load(mtl_terrain_multitex, "mtl_multitex.fx");
	bmap_to_mipmap(mtl_terrain_multitex.skin1);
	bmap_to_mipmap(mtl_terrain_multitex.skin2);
	bmap_to_mipmap(mtl_terrain_multitex.skin3);
	bmap_to_mipmap(mtl_terrain_multitex.skin4);
}
 
//function for terrain material
function mtl_terrain_multitex_init
{
	mtl.matrix11 = float(32);
	mtl.matrix22 = float(32);
	
}
 
////function for entity tga material
//function mtl_entity_alpha_init
//{
//	mtl.skill1=pixel_for_vec(vector(128,0,0),0,8888);
//}
// 
////action for entity
//action f_entity_default
//{
//	//material
//	IF(my._alpha_sort == 0){ my.material=mtl_entity_default; }
//	IF(my._alpha_sort == 1){ my.material=mtl_entity_alpha; }
//}
 
action icx_terrain
{
	my.material=mtl_terrain_multitex;
	my.polygon=on;
	c_updatehull(my,1);
}

---

set the my.transparent=on in the action nice_waves, but then the same problem occurs, so how can I get my water transparent without the discribed happenings??

Regards,
Frits