Yeah still broken for us in 5.4. Currently by far the most annoying unity bug we face, but hey they fixed crunched 24-bit textures in atlases! So some progress! The switching platforms I think is a pretty good clue. We do that constantly to make asset bundles for different platforms and that's often when it breaks. It's a huge workflow killer (requires a human to make sure the atlas cache didn't break each time we make bundles...for every platform...), but we lived with it for so long that's it's just kind of part of our unity life.