On the Switch Settings page, try setting the Management VLAN to 3, keep the switch uplink to Fortigate as native vlan 3, and ensure that on the Fortigate side, the native vlan is set to 3.
Unless configured otherwise, the AP will always pull a management IP address in whatever vlan is configured as native on the switchport that is connects to.
If you want your Meraki Switches to have management in VLAN 3, and the APs in VLAN 1, configure the Fortigate port to be native 3, allowed all.
Switch uplink to Fortigate to be nateive vlan 3 and allowed all.
Switch downlink port to AP,to be native vlan 1, allowed all.
Make sure all ip configuration is cleared from the individual IP address configuration on each device.
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