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No on-screen reason has yet been given. However it has been established that the TARDIS changes its appearance over time - the sign on the door changes color, for example, and the basic shape of the outside has never been consistent, either. In numerous episodes, such as "The Eleventh Hour", it's mentioned that the TARDIS does change her interior periodically and occasionally the exterior too. In "The Day of the Doctor", the TARDISes of the War, Tenth and Eleventh Doctors are seen side-by-side and they aren't the exact same shade of blue. So likely any inconsistency in the colour of the beacon light is related to this.