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Firstly there is no need to open multiple threads on the same subject.
As far as I am aware the remote controls all work on the same frequencies. There isn't a way to code one for one box and another on a different box.
Perhaps your girls might need to learn the use of their feet to walk to the STBs and change buttons, although that isn't a lot of use for all functions. If you can get some separation with the STB locations, so at least they are in different parts of the room, you might be able to experiment with the directional pointing of remotes so it's signal is then received only by one STB. Problem though is signals can reflect off some surfaces.