I cant seem to get the issue to repeat for me. Now it is always working.

Looking at the initial image that was posted with the problem all the edges are selected for them as well. Whatever the issue maybe I just happen to run into it my first stab the same way that the initial poster is doing.

<update> Found a way to cause a failure in one way. Depending on how close to the ends of each edge you are when you select. This is something I don't normally run into as I always try to pick the near the points that I want to have lofted together. However, in the case of this file the two open holes have different numbers of edges. The smaller one has 4 edges while the larger one has 8 edges. If you pick closer to the "wrong" end of the little short edges you can get strange twisting or even a failure now and then.