Ok so the picture below is a screenshot of showing what seems to be weird. I’m using a CG vertex shader to create a sine wave in the verts of a default plane. as you can see in the picture on the left(editor) i have the camera selected it shows the same image in the preview as the game window but in the editor the Y values are opposite to those displayed by the camera.
I also have a second camera parented to the first that when checking the preview shows the same as the main camera. but when rendering a cube that intersects with the plane into a texture it displays the cube as being occluded by the mesh that is displayed in the editor. If you zoom in you should be able to see the black mask displayed over the cube on the right is the same shape as what is visible of the cube on the left.
the shader deforming shader
http://pastebin.com/raw/q4a8zuhw