Are you using the new version of BSP? If so, I had these problems too. But they're easily fixable.
To fix the sky, make sure that the 'sky' flag is checked in the surface properties. Also, make sure the light value is at 1000 or something.
Make sure lit textures have the light flag set, and the light value at something fairly high. Feel free to compile with RAD at low, low settings to make it look about right.