Turn the 3D view to flat shaded, if they're truly black, then the extrusion may be turning the faces inside-out, so you have to select those faces and reverse the vertex order with Ctrl+Shift+F
Also, experimenting with the Auto Smoothing Group option, it seems that extrusion does keep
some smoothing groups, but not all, i think it only smooth shades the new faces but keeps the selected faces with the same smoothing groups they had before you extruded them, whereas turning that off will smooth shade any of the new faces and the faces you have selected
i'm thinking you extruded backwards or something
This could definitely be the cause of your problem, however