Why the dark objects won't be differenced from the base object? I made the objects by creating a cube in Object mode, going into Edit mode, deleting the vertices, clicking shift+LMB new vertices, making a face and extruding. 

On the light colored objects, I can add a Boolean modifier and set it to Difference, and it would make a hole in the base object the shape of the new object. However, inspite of these dark objects were made the same way as the lighter ones, when I try to apply a Boolean modifier, it deletes the base object.
In Edit Mode select all of your vertices and Recalculate the Normals. The option is in your Tool Tab in the Shading/UV's tab (Press the "T" key to toggle the Tool Tab on/off).