Issue with Drawing a GUI texture

So I'm creating a color edit mode for my game. I've determine how to do it and am working on implementing it in Unity. Thing is the images need some preprocessing to turn them into maps since photoshop aliasing of lines doesn't mean every pixel that needs a specific color is that specific color in the image.

Thing is I want to be able to show the changes as they are made so I am cacheing a copy of the texture and manipulating it. When I use that texture in GUI.DrawTexture(rect,texture) though it draws an opaque grey rectangle whereas if I use the original texture it draws the texture as it should be seen. How can I get the copy to render properly in the GUI.

      public float tolerance = 0.1f;
         public void GetPallette()
         {
             if (texture != null)
             {
                 if(ColorPallette.Count != 0) 
                     ColorPallette.Clear();
                 
                 Color temp = new Color();
                 if (tolerance < 1.0f / 255.0f)
                     tolerance = 1.0f / 255.0f;
                 int indexer = -1;
     
                 InternalTextureCopy = new Texture2D(texture.width, texture.height,texture.format,false);
                 InternalTextureCopy.SetPixels(texture.GetPixels(0),0);
                 
     
                 for (int i = 0; i < InternalTextureCopy.height; i++)
                 {
                     for (int j = 0; j < InternalTextureCopy.width; j++)
                     {
                         temp = InternalTextureCopy.GetPixel(j, i);
                         
                         if (temp.a != 1.0f)//Ignore pure alpha colors
                             continue;
     
                         //See if color is unique
                         indexer = isUniqueColor(ref temp);
     
                         if (indexer < 0)
                         {
                             ColorPallette.Add(new ColorMap(temp));
                             ColorPallette[ColorPallette.Count - 1].indexes.Add((uint)(i * InternalTextureCopy.width + j));
                         }
                         else
                         {
                             ColorPallette[indexer].indexes.Add((uint)(i
 *InternalTextureCopy.width + j));
                         }
                      }
                 }
             }
     
      public void OnGUI()
         {
             Rect rect = new Rect();
     
             if (texture)
             {
                 rect.x = rect.y = 0;
                 if (texture.height > texture.width)
                 {
                     if (texture.height > 250)
                         rect.height = 250;
                     else
                         rect.height = texture.height;
     
                     rect.width = rect.height * (float)texture.width / (float)texture.height;
                 }
                 else
                 {
                     if (texture.width > 250)
                         rect.width = 250;
                     else
                     {
                         rect.width = texture.width;
                     }
     
                     rect.height = rect.width * (float)texture.height / (float)texture.width;
                 }
     
                 rect.height = rect.width * (float)texture.height / (float)texture.width;
             }
     
             if (texture)
             {
                 texture = EditorGUILayout.ObjectField(texture, typeof(Texture2D), GUILayout.Width(rect.width), GUILayout.Height(rect.height)) as Texture2D;
             }
             else
                 texture = EditorGUILayout.ObjectField(texture, typeof(Texture2D), GUILayout.MaxWidth(250.0f)) as Texture2D;
     
     
             if (InternalTextureCopy != null)
             {
                 rect.x += rect.width + 10;
                 GUI.DrawTexture(rect,texture,ScaleMode.ScaleToFit,true);
             }
             
             if (GUILayout.Button("Get Pallette"))
             {
                 GetPallette();
             }
             
             tolerance = EditorGUILayout.FloatField("Tolerance: ", tolerance);
             EditorGUILayout.LabelField("Colors: "
 + ColorPallette.Count);
             
             for (int i = 0; i < ColorPallette.Count; i++)
             {
                 GUILayout.BeginHorizontal();
                  int g = 0;
                 //Highligh color channel in picture for easy analysis
                 if(GUILayout.Button("Highlight",GUILayout.MaxWidth(75.0f)))
                 {
                     uint Length = (uint)InternalTextureCopy.width*(uint)InternalTextureCopy.height;
                     int k = 0;
                     Color dummy = new Color();
                     for (int j = 0; j < texture.height; j++)
                     {
                         for(int l = 0;l < texture.width;l++)
                             if (j == ColorPallette[i].indexes[k])
                             {
                                 InternalTextureCopy.SetPixel(l, j, Color.white);
                                 k++;
                             }
                             else
                             {
                                 dummy = InternalTextureCopy.GetPixel(l,j);
                                 dummy.a *= 0.4f;
                                 InternalTextureCopy.SetPixel(l, j, dummy);
                             }
                     }
                 }
     
                 //Delete Color Channel Completely
                 if (GUILayout.Button("Delete", GUILayout.MaxWidth(75.0f)))
                 {
                     if (!ReplacementMode) 
                     ColorPallette.Remove(ColorPallette[i]);
                 }
                
                 //Replace Selection with another existing color channel - bring up window
                 if (i < ColorPallette.Count && GUILayout.Button("Replace", GUILayout.MaxWidth(75.0f)))
                 {
                     if (!ReplacementMode)
                     {
                         ReplacementMode = true;
                         ReplacementIndex = i;
                     }
                     else
                     {
                         if (ReplacementIndex == i)
                         {
                             ReplacementMode = false;
                             ReplacementIndex = -1;
                         }
                         else
                         {
                             ColorPallette[i].indexes.AddRange(ColorPallette[ReplacementIndex].indexes);
                             ColorPallette.Remove(ColorPallette[ReplacementIndex]);
                             ColorPallette[i].indexes.Sort();
                             ReplacementMode = false;
                             ReplacementIndex = -1;
                         }
                     }
                 }
     
                 if (i < ColorPallette.Count) //Needed because if a delete happens this will throw an exception since the count will have changed
                 ColorPallette[i].color = EditorGUILayout.ColorField(ColorPallette[i].color,GUILayout.MaxWidth(125.0f));
     
                 GUILayout.EndHorizontal();
             }
         }
         }
     
     //How I draw it