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@Dammit
As far as I can see it is because my calf muscle is now absorbing the force of my foots impact with the ground, rather than the cushioning in my normal shoe.
As I have learnt to run with the cushioned shoe my calf has never adapted to take this repeated loading cycle, so it gets tired, and then once fatigued it starts to hurt.
Therefore, if I keep going barefoot running the muscles will increase in strength, and it will no longer hurt.
If there is a way I could adapt my technique to avoid this process then I am all ears.