Harald Thanks. I've done more experiments and have narrowed it down to some code on our side, but still unsure why it's occuring.
On our SpineActors we have a script that holds references to different shaders. One of them is the basic tint shader. We change these are run time depending on the situation, but in this case it's I'm just testing with the basic tint shader.
When these actors are bundled, the tint shader on script is different instance to the one on the material (I can see via debugging). Setting the shader to the one bundled with the script on the actor is causing this issue. Using the one already assigned to the material works as expected. The shader is the same, so I'm not sure why it breaks when bundled? We're changing the shader on the sharedMaterials reference.
Unfortunately I'm still not able to upload a slice of the project as it's all very much linked.