If I understand correctly, you are using Velocloud for SD-WAN and Meraki MX to act only as a security appliance.
As Velocloud is providing the SDWAN between the sites - that is where you'll need to look for the issue.
My guess - it is an MTU squeeze in Velocloud. You can test this on two machines by temporarily lowering their MTU to something like 1300 and see if the issue goes away.
You need to find the name of the network adaptor being used with this command:
netsh interface ipv4 show subinterface
Then run this command to change the MTU (change "Local Area Connection" to the adaptor name above):
netsh interface ipv4 set subinterface “Ethernet” mtu=1300 store=persistent