The /interface bridge vlan section should only refer to ports in /interface bridge port and the implict bridge-to-CPU port which has the same name as the bridge itself. For more detail see http://forum.mikrotik.com/t/routeros-bridge-mysteries-explained/147832/1
The /interface vlan section defines objects which add a tag when passing traffic to the parent interface and removes a tag when receiving traffic from the parent interface.
/interface bridge vlan
add bridge=bridge1 tagged=bridge1,ether3,mgmt untagged=ether5 vlan-ids=99