This is an identical copy of the His and Her Owls that is quite popular on the thingiverse. However, the STL file supplied for that model does not work with MakerWare due to "inverted normals" on the female owl, meaning MakerWare was interpretting it as "inside-out" and couldn't render it.
I was able to fix the problem in Blender and re-export it properly. I successfully loaded it in MakerWare and printed it without issue on my MBot Cube II.
The right owl has inverted normals -- they're all facing inwards. So each "outer" surface of the female owl is interpretted as an interior surface. This is why it shows up weird in MakerWare (it's displaying the interior of an object, as if it was inside-out), and it doesn't print properly because it's not sure what to do. [Theoretically, shouldn't it print a cube with an owl-shaped hole in it? :) ]
I loaded the STL file in Blender and was able to verify this is the case. All I had to do was select all the faces of the right owl (switch to front-facing (numpad-1), orthographic view (numpad-5), and then 'b' for box select). Then on the left-menu there is a button for "Normals -> Flip Direction". That's all I did before re-exporting to STL.
I had similar problems with other models that I made in Blender: I created some surfaces/objects, but some of the normals were facing the wrong way and MakerWare freaked out and printed garbage. If you are making a model in Blender, you can switch to edit mode, open the properties menu ("N" key), select the "Normals->Show Face" button, and then set the size to 1.0 or higher. Any outer surface of your model should have the blue normal vector extending outwards into open air, not into the model.