I'm going to guess that your transparency setting for the bottom solder-mask layer is set to opaque, which prevents you from seeing the copper through the solder-mask layer. If you increase the transparency (make it less opaque; I don't remember if 0% or 100% is opaque), the masked bottom layer copper should become visible. When in 3D view, the transparency settings are found in the layers (shortcut 'L') dialog box. I'm not at my work computer to look it up, but you should be able to find the settings. Hopefully that is the problem.