Yes, I see the problem. I'll do something about this.
They are called Layout buttons, and each one remembers which panes are open in the main window, and some of their settings. Each layout also remembers which node to select in the Node List at the top left. When a node is selected, it finds it in the Network View. It doesn't go to a group, it goes to whichever node is selected.
If you close the Node Network in each layout, they should not open again in the current session. Although it's annoying, you only have to close it once for each layout.
I agree that it shouldn't do this if you have a separate Node Network window open.