Glad to hear it worked.
And sorry I originally replied to this quickly on a coffee break but I should probably explain why this is occurring.
A native vlan on a switchport tells the switch to treat any untagged frame coming into that port as the configured native vlan. And for any frames the switch receives destined for that port and tagged with that native vlan, it will strip the vlan tag off frames before putting them on the wire.
In this functionality, it's very similar to how an access port works.
Because you set the management vlan in the Meraki dashboard, the AP is sending out management frames already tagged with that vlan and is expecting to receive frames tagged with that vlan.
In your circumstance, because of the native vlan config on the port, the Meraki AP would have been receiving untagged management frames.