Hello Kumbirayi,
In your sample, PCf-Modes.mxd, the holes do not extend throughout the whole simulation window. See Lesson 5 – PhotonicXtal.mxd for an example. The holes are found everywhere throughout the whole X-Y Plane. If they aren’t there, the mode solver will look for a solution that is partly formed by the simulation window boundary. This is an artifact. This is what you describe as “funny like on some corner outside this fiber”. This is the reason the holes are put everywhere in Lesson 5 -PhotonicXtal.mxd . The holes must exist over a large area to properly confine the mode.
Please fill your exmpty space with photonic crystal holes, and you may see the real photonic crystal mode. It takes many holes to support it. That is why Lesson 5 uses script to create and place them – too many to do by hand!