It’s hard to know what kind of config your CRS is actually running. But since you mentioned multiple bridges it seems to be wrong … at least from performance point of view (only one bridge can be offloaded to switch chip, the rest are handled by slow CPU).
So start over by using single bridge (can span all ports) and use VLANs to “partition” your CRS.
And here’s a very good tutorial on how to do VLANs on MT the way which allows CRS to run wirespeed: http://forum.mikrotik.com/t/using-routeros-to-vlan-your-network/126489/1