Depth Test Issues

I get strange depth test issues if I use one of the transparent or fade shader versions. At least I guess it has something to do with the depth test.. It's confusing because it worked some weeks ago.. The image shows a part of a landscape that I generate. The landscape and water is created with multiple meshes. To upper image looks like it should (but without the alpha channel) and the lower shows the issue. I already tried to play around with the ZWrite and ZTest settings in the shader but that was only trail and error without success