When Blender 2.46 was released, the bundled X3D exporter was updated as well. As a result, the exported X3D files were no longer recognized by Shapeways. We're happy to announce that we've fixed this issue!
There are now two ways to get your design from Blender into Shapeways: either by exporting as X3D or as STL. Both fileformats have a tiny gotcha that you should be aware of: the default Blender unit is interpreted as 1 meter. Be sure to scale your design down before exporting, or you might just find it a tad too expensive to print