[mlpotgieter]

Ok I sent this q to the "support ninjas" and got a response. It seems that this is expected behaviour but there is a feature request in that will allow more control over how the ends of lines are routed.
In the mean time it was suggested that objects, like a rectangle be grouped to the stencils and put over the ports. This way the line is connected to the edge of the rectangle and not to a magnet. Seems like a reasonable work around, and most of the stencils that come pre-installed with Omnigraffle are made like this. I have uploaded a couple of networking device stencils to Graffletopia and these will all need to be modified but this is a one time thing which should resolve the problem.