Problem in Visio 2003 SP3 when saving a document as SVG
Arrow heads disappear for two reasons:
a) marker-end:url(#); bad links for marker type references are generated occasionally >:(
b) style="overflow:visible;" missing, leading to cropped arrow heads on e.g. Batik
b) is easily patched by replacing orient="auto" with orient="auto" style="overflow:visible;"
a) is harder since it is not obvious which marker type was intended
As a matter of interest, what you using as an SVG viewer?