I have pretty much similar problem with vpn. Bandwidth test between mikrotiks shows great speed, but when it comes to speed between 2 devices behind each of mikrotik - speed drops drastically. Emils from support was on this problem, did nothing, made couple strange suggestions and then promised to look one more time and disappeared for over a month now. Support ingores all follow letters, meanwhile we’re suffering from low vpn speed and noone can help even with a hint on my config. That’s another end of 160 employees company I think. VPN speed wont go higher than 20 mbps, when real speed between routers is greater then 60 mbps even with encryption.
[Ticket#2016052266000207]