Hi @drawntoresearch,
Thank you for sharing the details. As the expert suggested, could you let me know your Illustrator version and OS? It would also be helpful to know whether this happens with all files or only specific ones. If possible, a short screen recording showing the copied elements losing their relative stacking order would make it easier for me to review with the team.
In the meantime, you can try resetting Illustrator preferences after backing them up. Once you've done this, please let me know if the issue still occurs.
Looking forward to your update,
Abhishek