The hole is closed because the software Shapeways uses will automatically close all holes, in doing so it may delete other parts. Your model may just need to be repaired manually.
It may be easier to send your STL file by PM or my email address.
Sorry I was not able to fix your file.
I have uploaded the image so you can understand what is wrong.
Models have to have a thickness, not just a 'skin'. The models normals need to be pointing in the right direction. So Shapeways knows which is inside and outside. http://en.wikipedia.org/wiki/Normal_%28geometry%29
Models need to be manifold or watertight. In other words if you filled the inside of your model with water it would not leak. By the inside I mean inside the walls, which must have minimum thickness dependent on the material.
The other thing is the smoothness of your model. The amount of facets you have around circular objects. Try to increase this.
It may look smooth in your software but the file you upload may be different. Open your model In Netfabb WYSIWYG
The image is a screenshot of Autodesk Inventor Fusion http://labs.autodesk.com/technologies/fusion which is free
The Microsoft Windows compatible technology preview executable expires on April 1, 2013.
The Mac App Store version of the technology preview has no expiration date.