I cannot post the Shader code itself, but I was wondering if there is some common problem that occurs for Shaders where this would happen.
Looks to me you're discarding pixels in a pixel shader, or having multiple passes where you end up with Z buffer fighting due to previous pass overlay. Sorry for the vague answer but you don't provide much information. :)
Are you messing around with the mesh in any way? Just considering there might be some issues if not all data channels are populated... It looks linked with vertex data from the shapes.