I can't be sure, but I think it has to do with the placement of your UV islands (as well as some of their shapes). As you can see from the image, the normals are all correct, so I think it must be UV related. I think you will need to find a way to ensure all the faces are in the 1001 space (light grey square), and that all faces that need to be "even" (squared off and such) are done so accordingly.

Also, I'm not sure if it's related, but there is a hidden object in your scene called Plane.003 - is that supposed to be there?

I can't be sure, but I think it has to do with the placement of your UV islands (as well as some of their shapes). As you can see from the image, the normals are all correct, so I think it must be UV related. I think you will need to find a way to ensure all the faces are in the 1001 space (light grey square), but not overlapping, and that all faces that need to be "even" (squared off and such) are done so accordingly. Unfortunately, it seems most (if not all) of the cubes comprising your "megacube" will need adjustment this way.

Also, I'm not sure if it's related, but there is a hidden object in your scene called Plane.003 - is that supposed to be there?