As far as I can tell, this isn’t a bug in L2TP, but rather a problem with how your rules are written. You can test this by trying to SSH, PPTP, or WinBox into MikroTik on either wan IP. You will most likely find that one IP works, the other does not.
When a packet goes to leave, even if it knows to use ISP2’s IP, if the routing rules tell it to go out ISP1, it will head that way.
If you look at the Layer3 part of the Packet Flow Diagram, you will see that Local Process OUT goes directly into a Routing Decision, without passing through prerouting, so all your mangle rules and packet marks never touch it. Nowhere in your route rules do you tell it that ISP1 source IP always goes out ISP1, and ISP2 source IP always goes out ISP2.
I have been successfully running dual WAN with L2TP on both interfaces since 5.4 (just after I started on PCC). I posted my config for doing so over in this thread:
http://forum.mikrotik.com/t/l2tp-tunnels-with-multiple-internet-connections-issues/49379/1
I hope it helps.