Yesterday I stumbled upon another hidden feature of Batik, when I noticed that the Visio diagrams didn’t show their arrowheads in the generated jpeg. It seems this is caused by an inappropriate markerWidth/Height and viewbox. According to the SVG specification you need to make sure the marker does not overflow it’s viewport.
A quick fix for this problem setting the overflow to visible on the marker.
<marker id="mrkr1-7" class="st2" v:arrowType="1" v:arrowSize="2" orient="auto" overflow="visible" markerUnits="strokeWidth" />