If your /ip firewall filter rules contain an action=fasttrack-connection connection-state=established,related rule provided by default, you have to make sure that the L2TP traffic in both directions will never match this rule. The point is that all but few packets belonging to a fasttracked connection do not pass most of the firewall stages, including the mangle rules, so they are routed out your regular WAN as they could not get the routing mark. And you have to take care about both directions because a packet in either direction causes the connection to be switched over to fasttracked mode. So first just disable the rule to see whether it is the cause (and establish a new connection to test because already existing connections won’t be affected by the change); if it helps, add in-interface=!l2tp-out1 out-interface=!l2tp-out1 to the action=fasttrack-connection rule to keep the advantages of fasttracking for usual traffic and prevent fasttracking from happening for the VPN traffic.
You can also use a more generic setup if you want.