I've been doing some research, and I think that I've discovered the problem. When ever a new starbase is built, or an existing one is upgraded, the glowing thing switches location with another particle. Usually its one of the exhaust clouds, and if you look closely at the hole where the glowing thing should be, you can see the exhaust cloud in it. I have a screenshot, but I can't seem to get it to show up. I've also seen it replace one of the little flashing lights, with the light ending up inside the hole. As I said earlier, this seems to happen everytime a new base is built, or an existing one is upgraded. You add trade to the base, and all the glowing squares in the correct places will switch somewhere else, and all of the squares in the wrong places go back to the correct locations. Hope this helps.