The easiest/quickest way to turn the JCS purple background into pure black is that I just edit the existing pallette value to pure black on GraphicsGale (the free version should do it's job just fine, the commericial version only allows ICO and GIF access which you don't need). That means you don't need to use flood fill at all, and won't have the possibility of accidently leaving an area non-transparent. The image is palettised (the colours are assigned to the pallette board, which goes up to 255. BMPs/GIFs are always palettised, and PNGs - not if you set them to 24 bit colour mode), allowing me to do that.

However, when I'm making/editing a tileset, I never use pure black for the transparent background, because it makes outlines much harder to see.