Are you by chance using IKEv2 and have multiple subnets selected? IKEv2 on Meraki only supports a single subnet combination. You have to use IKEv1 if you need to support multiple subnet combinations. I echo your sentiment that MX is weak in the third-party VPN area. When I tend to do, when I need to link orgs, is put an MX from each org next to each other in one central site, add static routes between them, and reidstribute those static routes back into AutoVPN on each side. That works rock solid.
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