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I'm using SkeletonAnimation. Another variable I forgot to mention is that I'm manually exporting the atlas files in Spine. We have a lot of color variations for all our units, so we setup a folder and skin for each color. By manually exporting our whole Units folder, each atlas is per color. So we don't need to load all 10 colors when only 2 are present.
Apologize for the information overload, but I did a lot of troubleshooting last night. Below is what I found.
I tested with a single blue unit and I don't see any issues.1 red, 1 blue = flickering. 2 blue = flickering.
I noticed that red units have 1 atlas and blue units have 2.
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There are some parts of the animation that are shared and don't have a skin, like the thrusters you see changing draw order in the above image. It looks like the thrusters for blue units are using the red unit atlas. I tried taking out the neutral parts from the color atlases and just making a neutral atlas for thrusters and other shared parts, but I still see the flickering draw order issue. Can you not layer parts from different atlases between each other? It seems like that's the root of what's causing this strange behavior.
Small correction, issue only stops when I put a blue unit on their own distinct Sorting Layer in Unity. Once I add a second blue unit the flickering comes back. Seems like a confirmation that something funky is going on with how it draws itself.