Did you use the wizard to build the L2TP tunnel?
Cause your issue looks kinda like this one, so the MSS clamping value might be the problem: https://community.ubnt.com/t5/EdgeMAX/Huge-problem-with-MTU-solved-it-wasn-t-MTU-it-was-TCP-MSS/td-p/1228239
Educational link: https://fredrikjj.wordpress.com/2014/08/10/fragmentation-mtu-mss-clamping-tunnels/