Ah, thought it looked vaguely familiar.
BOM is not exactly portable, and X3D is UTF8 by definition (and I just checked that the standard also requires that the file "starts with"
the <xml version... header, which would seem to expressly forbid a (redundant) BOM (or any other bytes) before it).
As far as verifying that the file without the BOM uploads correctly, you can easily do this yourself just by clicking on the "upload" button
in the top left corner and selecting the file on your local disk. After a short wait, you should see both a WebGL-based 3D preview and
a table with the object size as perceived by shapeways. (You will also see the cost stated for production in the various materials, and
also whether the object is fit for printing - in particular, there are material-specific minimum requirements for the diameter of the cylindrical
connecting "wires" in your model.)