RenderTexture varying behaviour - Unity 5

I've got some code that uses GL calls to render white triangles on a black background into a RenderTexture. This texture is then used in a shader.

This works in some configurations, but not others:

• Running in the editor it works, although I had an oddity where the texture would blank on every keypress/release that came and went away with an editor restart.

• Running it via a windows build produces a texture where the triangles are transparent rather than white.

• Running it in browser plugin or webGL builds produces an entirely black texture (I've verified that it's being cleared by the GL calls by changing the colour).

So, can anyone shed any light on why I'm seeing these variations? Am I supposed to be setting the RenderTexture to a specific format or something?

Extra Info: The drawing occurs in the update. I've tried moving them to a camera precull/prerender callback but this doesn't seem to work at all. The GL code itself is:

 Graphics.SetRenderTarget(shadowMaskRT);
 GL.PushMatrix();
 GL.LoadPixelMatrix(0, shadowmapSize, 0, shadowmapSize);
 GL.Begin(GL.TRIANGLES);
 GL.Clear(false, true, Color.black);
 GL.Color(Color.white);
 
 for (int i = 0; i < tris.Length; ++i)
 {
     GL.Vertex(new Vector3(verts[tris[i]].x, verts[tris[i]].y, 0.0f));
 }
 GL.End();
 GL.PopMatrix();
 Graphics.SetRenderTarget(null);