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Which particle system is this? Instancing with custom geometry uses the transformation matrix of the particles, maybe it's not available, or not transferred properly. Could you please send me a scene to check?
I need a little more information.
1) What are you using to generate the particles.
2) How are you assigning the custom geometry.
Hey, is your issue solved? If not, could you please give me more details, or maybe a simple scene to reproduce the issue with?