The channel ordering in live:cut depends on which channels were selected for the live:cut project in the first place. For instance, when you have four channels selected in just:control Just Control, then you will have four channels in your live:cut project. Channel ordering goes from top left to bottom right, as can be seen in following screenshot.
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In case you have four channels connected in just:control Just Control and you are only using two channels (in this case, Channel1 and Channel4) for live:cut, then the channel ordering changes accordingly. Please see screenshots below (Channel2 and Channel4 are connected but not active in live:cut mode).
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