Found a post talking about the dual switch issue now:
http://forum.mikrotik.com/t/rb2011-vlan-slow-lan-speed/133125/1
“There is a way to configure the device to have all ports switch together and yet be able to use VLAN filtering on a hardware level, though this solution has some caveats. The idea is to sacrifice a single Ethernet port on each switch chip that will act as a trunk ports to forward packets between switch chip, this can be done by plugging an Ethernet cable between both switch chip, for example, lets plug in an Ethernet cable between ether5 and ether6 then reconfigure your device assuming that these ports are trunk ports”