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Yes, I am pretty sure that the quantum-openvswitch-agents are running in the second setup; I have restarted them on both hosts numerous times.

I have also compared "ovs-vsctl show" on both setups (the working and the broken one), and they both looked identical -- this is from the compute node:

Bridge br-int
    Port "vnet0"
        tag: 1
        Interface "vnet0"
    Port br-int
        Interface br-int
            type: internal
    Port "vnet1"
        tag: 2
        Interface "vnet1"
    Port patch-tun
        Interface patch-tun
            type: patch
            options: {peer=patch-int}
Bridge br-tun
    Port "gre-3"
        Interface "gre-3"
            type: gre
            options: {in_key=flow, out_key=flow, remote_ip="192.168.133.113"}
    Port patch-int
        Interface patch-int
            type: patch
            options: {peer=patch-tun}
    Port br-tun
        Interface br-tun
            type: internal
ovs_version: "1.4.0+build0"

and this is from the computing node:

Bridge br-int
    Port "tap9885f7e6-c8"
        tag: 1
        Interface "tap9885f7e6-c8"
            type: internal
    Port patch-tun
        Interface patch-tun
            type: patch
            options: {peer=patch-int}
    Port "qr-5dd26f35-67"
        tag: 1
        Interface "qr-5dd26f35-67"
            type: internal
    Port br-int
        Interface br-int
            type: internal
Bridge br-tun
    Port "gre-2"
        Interface "gre-2"
            type: gre
            options: {in_key=flow, out_key=flow, remote_ip="192.168.133.112"}
    Port br-tun
        Interface br-tun
            type: internal
    Port patch-int
        Interface patch-int
            type: patch
            options: {peer=patch-tun}
Bridge br-ex
    Port br-ex
        Interface br-ex
            type: internal
    Port "qg-6bcaf016-b1"
        Interface "qg-6bcaf016-b1"
            type: internal
    Port "eth2"
        Interface "eth2"
ovs_version: "1.4.0+build0"

Where would the l2 agent get the information on how to create/modify the flows?