Don't know if they may help you. But I had a similar problem with FOP2 running on Asterisk 11.2.1 w/FreePBX 2.11.0.0beta2.2
I would try to remove/add extensions to/from a specific queue and nothing would happen. As it turns out I have declared in Queue static agents.
When I removed all agents from the queue in FreePBX GUI or in queues_additional.conf and left the queue empty in so far as Asterisk was concerned. And then restarted FOP2
I was able to use FOP2 to add/remove extensions to/from queues as I pleased.
Not sure if my experience will help in your case, but thought I share it in the off chance it does.