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I don't know if you've solved this problem yet, but this sounds like it could be an issue with face normals. I don't know how well you know the 3D jargon, but basically, you have to choose which side of the face is "outside". If it's wrong, "outside" is "inside", and depending on the program, those faces are either invisible, or black, or get lit as if the light was coming from the opposite direction.
Try recalculating normals (Edit more, choose faces, Ctrl+N; or from one of the sub-menus of the Tool Shelf on the left side of your 3D view).