I ve issues about texture atlas , I ve made my texture atlas in blender, I ve unwrap manual , then organize the UV manual and then export to unity.
in the firts pic everything seems allright, I use Pack island,I think that that is a problem, broken the scale or miss something (see the paint section) , I ve apply the scale of every object and then bring em to unity engine... I ve Loaded the meshes on Unity's heritage and Texture to a folder.
The process in blender and (then paint :D to think the solution ??)