Basically, Inkscape is remembering what the last fill/stroke settings you used were. If you find this annoying, you can make Inkscape use a standard color/fill for each tool instead; go to Inkscape Preferences and navigate to Tools -> Shapes -> * and set from "Last used style" to "This tool's own style".
Actually, it would be useful if you could have each tool remember its own last used style. I have it set on "last used style" but it's quite annoying if I am switching between the freehand tool and the calligraphy tool, because when I am line drawing I want a coloured stroke and no fill for the freehand tool, but a coloured fill and no stroke for the calligraphy tool.
Much as I'd be happy to write this in myself, I am on far too many projects as it is, so I merely ask that you bear this idea in mind.