I have done a few pens that have had the look you are describing. I have been told that it is the fibers or cells of the wood that are causing that look. I don't know if all wood, but at least many woods have the cell structure open enough so that you can take a piece of it and blow through the wood. You are actually blowing through the cells or tubes of the grain. When you sand, these cells get cut into and when you are sanding along the length of the "tube" it will have this look when it is sanded open. I know I'm not using the proper terms or words for all of this, but that is the gist of what I have been told. I'm sure I'll be corrected if I am wrong on this.
This info is from my wife who has been taking woodworking classes at what is supposed to be one of the top programs in the country for making furniture. The first class discussed wood composition and they talked about the grain and how fluids go up and down these tubes. Since you have the same look at opposite sides of the wood I would assume this is the cause of that. The first pen I did with this effect threw me for a loop. I saw this after applying the finish and ended up sanding it down all over again and redoing the finish only to get the exact same look. I asked my wife if those were scratches (needed a second opinion, and I was very new at all this) and she told me about this effect.