This was a change with version 3.0 vs earlier versions....
as I recall..... on an AP that I coverted from v2.9.51 to v3.something where (in this case) the Ethernet was bridged to the wireless interface....
... suddenly the queues no longer applied (or at the least the traffic counters did not advance) and forward firewall rules were not being applied.
........after extensive beating of head against my desk, and searching this forum, that was the answer that I found.
Checked the box, and both issues were corrected.....
I've read the docs which try to cover this question a couple of times...
http://www.mikrotik.com/testdocs/ros/3.0/qos/flow.php
I can read the words, but can not quite understand what they're saying about the subject....
The v3 docs do not yet even cover the bridge configuration attributes.
Perhaps a future version of the docs will better define the situation.