Comment 2 for bug 588132

IMHO these differences are not bugs - the markers are rendered according to their definition in 'share/inkscape/markers/markers.svg'.

Connectors connect with the nodes of the connector lines to the connected objects. The precise location of the (stock) markers at the start and end nodes of the connector lines depends on how it is defined in the SVG code of the 'template' marker. As you see markers can differ with regard to their position relative to the node they 'mark'. It seems that 'TriangleIn/Out' was more intended to be used as mid-marker, whereas 'EmptyTriangleIn/Out' is positioned similar to the plain arrow heads and better suited for start and end nodes.

You could create new custom markers if the stock markers provided by Inkscape lack symbols you need. Or maybe someone can contribute a set of start and end markers that are better suited to use with connectors.

Note: markers in Inkscape (try to) follow the SVG 1.1 specification.

References:
<http://tavmjong.free.fr/INKSCAPE/MANUAL/html/Attributes-Stroke.html#Attributes-Stroke-Markers>
<http://tavmjong.free.fr/INKSCAPE/MANUAL/html/Customize-Files.html#Customize-Files-Markers>
<http://www.w3.org/TR/SVG11/painting.html#Markers>

Proposing to close as 'Invalid' or mark as 'Wishlist' for new stock markers specially suited for connector lines.