I remember some LaTeX users encountering the bounding box problem too when using EPS graphics, and, if my memory serves me, one solution was that a rectangle should be created around the content of the image (set fill to "none" and line to either "none" or, if that doesn't work, "white" or another suitable color). Now bounding box shouldn't be miscalculated, but coordinates set by the rectangle as the largest object on the page will be used. Of course, you'll have to do this using some vector editor like Inkscape or Adobe Illustrator.