Hi,
1.using an unattend.xml file with copy profile
Did you mean that you are using the StartLayout.xml which was exported from the VM(you've customized before)?
2.However when I clone and then sysprep the VM
Per my knowledge, Clone is not officially supported since it might have some problems. The normal methods to keep customized startlay out is to add the .xml file before sysprep.
Reference link:
https://www.joseespitia.com/2016/06/27/customized-a-windows-10-start-layout/
Please note: Information posted in the given link is hosted by a third party. Microsoft does not guarantee the accuracy and effectiveness of information.
Hope this helps and please help to accept as Answer if the response is useful.
Thanks,
Jenny