I also encountered the arrowheads problem. It is an old problem of OmniGraffle. I tried a solution suggested by Vincent22 here in
SVG export/dot import.
But then the renderer on wikipedia commons only shows one half of the arrows:
http://commons.wikimedia.org/wiki/Image:Pn_overgang.svg, although Firefox will display them as I had intended.
Lots of my Omnigraffle drawings have arrowsheads on them, and I would like to export them to SVG, without having to manually tinker in code that I do not really understand.