RTF is a global modification that replaces all towns in the game.

You need a black transparency. That is, 0,0,0 for RGB and the alpha channel should be fully transparent.
When you use the eraser in Paint or Photoshop, it creates white transparency (ff,ff,ff for RGB, but with an alpha channel), and the game interprets this as a white color. As a result, you get a lot of white spots.