Try opening your model in Neffabb. Go to part, rotate, look at the x,y,z icon in the bottom left corner, as a guide then pick the axis you require to rotate and pick the right angle. then just go to part again and export part. Then just update your original file to Shapeways.
When you draw something in 3D, there is an 'X' 'Y'' and 'Z' coordinate system. 'X' is across as it says, across the screen as you draw. 'Y' is up and down as you draw and 'Z' is coming straight out of, or going into the screen as you draw, which you can not see untill you change your point of view. So basically the 'Z' is always up or vertical. so even in the software you used to create your design will allow you to rotate your drawing in one of the axis to align your drawing with 'Z' up. Dont forget 'Z' is always up.