I had/have similar issue, described here.
Only workaround I find is that you need to add always manually the outgoing policy. (which is very inconvenient in case of roadwarriors)
I was also in contact with Mikrotik support (ticket number is Ticket#2015061266000262), where they stated in case both client and server are behind NAT, then L2TP/IPsec will not work. This is a limitation of Mikrotik I guess, because with SoftEther it works.
Let’s hope there will be an improvement in v7.