Occasionally Contours becomes confused and loops back to first stroke

Even with Cyclic disabled, occasionally it loops back and connects the first and last strokes:
http://cl.ly/RHdH

If you look closely, you'll see it has also disconnected an intermediate loop: 
http://cl.ly/RI4j

If this can't be solved through the algorithm, we may need to implement a way of manually specifying the first loop, similar to extruding vertices.
