Pixel errors when drawing to Render Target with shader

So, I'm building a system to allow sprites to have manually selected colour palettes from within the game. To achieve this, I'm rendering sprites through a shader using Graphics.Draw onto a render target. Then, I'm using that render target in the game as a sprite sheet.

I've set up a system so sprites can use up to 3 colours by encoding them in the RGB channels of the texture, allowing each colour to be replaced independently:

http://i.imgur.com/UhXuqPc.png?1

This, when put into my current shader, produces this image:

http://i.imgur.com/vveYbEe.png?1

You'll notice that a bunch of pixels appear incorrect. I'd like to know why this would be the case.

Here's the relevant section of my shader code:

             fixed4 _Color1;
             fixed4 _Color2;
             fixed4 _Color3; 
 
             fixed4 frag (v2f i) : SV_Target
             {
                 fixed4 col = tex2D(_MainTex, i.uv);
                 fixed4 c;
                 c.rgb = (col.r*_Color1.rgb + col.g*_Color2.rgb + col.b*_Color3.rgb);
                 c.a = col.a;
                 return c;
             }

And here is where it's applied in the C# script:

         RenderTexture.active = rt;
 
         GL.PushMatrix();
         GL.LoadPixelMatrix(0, rt.width, rt.height, 0);
         Material m = new Material(Shader.Find("SpriteColour"));
         m.SetColor("_Color1", s.colourMapR);
         m.SetColor("_Color2", s.colourMapG);
         m.SetColor("_Color3", s.colourMapB);
         Graphics.DrawTexture(new Rect(0, 0, s.sheet.texture.width, s.sheet.texture.height), s.sheet.texture, m);
         }
 
         GL.PopMatrix();

I should also note that these strange artefacts do not appear if I map the colours to their base RGB (essentially leaving the texture unchanged). The only thing I can think is if the changes are happening on certain pixels more than once, but I can't see why that would be.