Bake selected and dual lightmaps, near and far changing.

Hello again, after recently solving my bake selected issue I have now stumbled into a new issue. I managed to resolve this with some faffing around, however when it came to re-bake my lights to a higher resolution the issue persisted. I would like to stress that I had everything working fine with near and far lightmaps working correctly after baking each sub-scene.

Basically, I have four separate instances of the same environment, with some subtle changes, all in one scene. They each have their own directional light with different positions and colour. All other settings on the directional lights are the same. I select a sub-scene, hide the other lights and bake selected, the scene that is baked looks fine with properly operating shadows, however the other scenes then have issues with their near and far lightmaps not matching up.

The image below may provide a better explanation than I can. In this instance I bake my Spring sub-scene, (the one seen on the right of the image). Once baked, I then hide the all lights but the Autumn one, then bake the autumn sub-scene. Once baked the Autumn sub-scene is behaving properly, however, the Spring sub-scene's near and far lightmaps produce strange results.

So far I have noticed that the shadows in the far lightmap are the same as the near, with lighting disabled.

I had this working 100% previously, I am not sure what I did to fix it (I should have had the foresight to write down my processes and settings), but now I am having the same issue again.

The only thing I have changed on the lightmap bake settings is the resolution, I will paste all my settings below.

Thanks in advance for any help.

Cory.