15 February 2017
I don't do a lot of baked lighting stuff, so I'm not sure what might be wrong. I can only see one image in your post (sorry, the forum markup is kinda terible).
One thing you could try is to switch the meshing mode to "Culled" instead of "Greedy". That might even out the UVs.
PicaVoxel is really meant for dynamic voxel models that can be changed at runtime and so probably isn't the best choice for static geometry anyway. You might want to try exporting as .OBJ from MagicaVoxel and seeing if that works better for static/background objects.
If you can, please zip up the project and send it to firstname.lastname@example.org and I can take a closer look.