Multiple bridges is generally a bad idea as you will loose the hardware-offloaded wirespeed switching on all but the first bridge, and interfaces may only be assigned to one bridge.
Without seeing the configuration it is impossible to say what you have done wrongly. Some useful information http://forum.mikrotik.com/t/routeros-bridge-mysteries-explained/147832/1 and http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1