If you are on 6.41, it looks like you miss the Bridge/VLAN configuration.
There you tells if VLAN should go tagged or not to port/bridge.
Look here: http://forum.mikrotik.com/t/sofware-vlan-bridge-on-ruteros-explained/122534/1
and Sindys post here:
http://forum.mikrotik.com/t/sofware-vlan-bridge-on-ruteros-explained/122534/1
example
/interface bridge vlan
add bridge=bridge-all-vlans vlan-ids=10 tagged=bridge-all-vlans,ether2,ether3 untagged=ether1
add bridge=bridge-all-vlans vlan-ids=20 tagged=bridge-all-vlans,ether1,ether3 untagged=ether2
add bridge=bridge-all-vlans vlan-ids=30 tagged=bridge-all-vlans,ether1,ether2 untagged=ether3