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Every so often planets and the sort are unable to be unpinned from the empire overview icons and stay there even if I unpin and then re-pin and again unpin. I've not found a way around this problem. Just making a note of a bug in the game at this time.
Check to see if it has a star base or a fleet that is pinned. This usually will keep the planet "pinned".
And short of messing with the .ini file there is no way to make it stop doing it automatically.
You can still unpin them if you right click on the tack at the top of the fleet manager. This will, of course, unpin all planets, but if you have more planets than your screen resolution can show it's often less annoying to repin the few important planets and neutral wells than your fleet manage jumping back and forth everytime you select a fleet.
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