Hi,
I have half the ports of my RouterBoard configured as slave ports to port 2, which is configured with the main network of the router (x.x.x.x.49/29). I've noticed that if I have a device running on any of the slave ports, none of the mangle firewall rules seem to pick up any packets. If a configure a bridge, and set IP firewall to on, then it starts picking up packets.
Is a bridge + IP Firewall required to mark packets and use the Queue functions on those ports?

Thanks.

Yes, although maybe (depending on the rb model and types of mangle rules) switch rules could assist you

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Also to be clear an enslaved port is L2 connected to the master and all remaining slaves. Thus an L2 request that does not require the Router will be forwarded by the switch and ignore all the rules as they are L3.