The black part looks like you did not pull your dark slide all the way out.
The color difference is because of the software. It cannot think intelligently - actually see your picture and analyze it; it is just programmed to make a bunch of pixels of various colors average out a certain way. You need to use your eyes to perfectly color balance something, or if you do use automation, a neutral gray card should be the target. Changing color balance in Photoshop is the same thing as changing it in your enlarger, so don't feel weird about that. We all have to tweak color balance in anything but bright, clear, middle-of-the-day sunlight, whether we do it in the camera or in the darkroom.