When you are doing the fill, are you still in the Channels Palette? That would be the only way that I can think of where you'd be filling in black. After you've made the selection so you have the "marching ants" go back to the Layers Palette to do your fill. On an image like this one, I'd usually do a new layer for each selection. That way I could play with filters and the blending mode for each filled area.