I didn't mention the WAN throughput because it's not a problem, but the Auto VPN tunnel.
Anyways, I spoke to Meraki Support on a different issue on the other day, and I brought this strange behavior, we took some captures, here is what we have found when executing ping.
+ Meraki to the Internet is fine.
+ From an endpoint sitting behind Meraki MX/Z to the Internet is fine.
+ From Meraki to Meraki (both WAN & inside IP) is fine.
- From an endpoint sitting behind Meraki MX/Z to one of the Meraki spoke is unstable.
- From an endpoint sitting behind a Meraki spoke to another endpoint sitting behind another Meraki spoke is unstable.
He downgrade the firmware, the issue is gone. He said he would check and monitor with other peers because it's recently released and not many customers have upgraded yet.