I have a similar issue, except it is between C9300 & MS390 stacks. The allowed trunk ports match but the one that doesn't is the native vlan, but I haven't changed the value yet as they are working as intended and they are a critical piece of our infrastructure and I've yet to pluck up the courage to make a change. If you view the ports in the meraki dahsboard, what does it show under the vlan mismatch info when you click on Warning: Vlan Mismatch under the CDP/LLDP value in the status section? Image is taken from my dashboard, but I can't show the info under the warning pop-up
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