@o4kapuk I've noticed that I'm getting a couple of these messages in the console for each room I look at:
[.WebGL-0x223445f49c00] GL_INVALID_OPERATION: Feedback loop formed between Framebuffer and active Texture
This would explain the issues, if screeps is using some sort of render-texture and there's a loop then I can definitely see how it would cause this problem with rendering order.
Additionally, there's another issue that's even more annoying which I'm noticing more and more lately - sometimes some structures are invisible in certain rooms. It only seems to affect complex structures like storage, factory, terminal, labs and nuker, and I've only noticed it for structures under ramparts. I think this is the same bug manifesting in different ways. They momentarily become visible when zooming in/out, but it's just a brief flicker and then they're gone again. As with roads, it seems to persist after navigating to other rooms and across a full refresh and even after closing the browser. Again, an issue with a texture loop would seem to explain this.