Thanks, this is making sense with my intermittent issues. I did some digging and the vlan that the server is on has a static route configured for the DNS server on a different subnet and that other subnet is using the L3 switch to reply going around the Meraki. Unfortunately to fix this there will probably be down time while I cut over the vlan from the L3 switch to the firewall. I was hoping I could build the vlan with a different gateway, trunk the vlan to the meraki, cut over the gateway on the DNS servers from the core, remove the static route. but it wont let me build the new vlan because it overlaps with the static route (as expected) I will just wait for after hours and make the changes probably.
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