I am experiencing the same problem.
I have my pfSense box connected to StrongVPN and I see this in the logs:
WARNING: 'link-mtu' is used inconsistently, local='link-mtu 1558', remote='link-mtu 1562'
WARNING: 'mtu-dynamic' is present in remote config but missing in local config, remote='mtu-dynamic'
When I put tun-mtu 1500 in the Custom Options, like you the warning changes.