Did you remove your IPsec traffic from fasttrack? I just posted my config example for privateinternetaccess.com VPN (http://forum.mikrotik.com/t/privateinternetaccess-com-ipsec-ike2-config-with-port-forwarding/131568/1) connections where you can see it.
I had similar issues - speeds seemed fine initially but the connection were unstable and I got regular timeouts.
With the fasttrack exceptions I am getting now 287/48 MBit/s on a 300/50 connection. (with an RB4011)