When I build for Windows from my desktop everything looks as expected. When I build using Unity Cloud Build the artwork found in four large 2048x2048 atlases (made using TexturePacker) do not work correctly. See the attached screenshot:

What version of Unity are you building with? And are you seeing issues for any other sizes or just the 2048’s?
When I build locally and things work I am using Unity v5.4.1f1. When building using Unity Cloud Builds I am using “Always Use Latest 5.x”. It only appears to happen with the 2048 textures.
Can you try building with the same version of Unity in Cloud Build (i.e .5.4.1f1) and let me know if you still see this atlas problem (“Always Use Latest 5.x” currently is 5.5.0f3)?
No success specifying Unity 5.4.1f1 explicitly. Results are the same.
Are these atlases being generated at build time, or are your exporting them with texturepacker and committing them to the repo?
They were generated months ago and committed to the repo. Both methods are using the same atlas.