I had a similar problem where often the intercoms were not ready, but then sometimes they would just magically work.
What I found is that the sipproxy service was enabled on my director. Sipproxy and freeswitch both try to listen on the same TCP & UDP port number. Whichever one grabs it first at boot time works, and the other is broken. For the new communications agent, you want freeswitch, so make sure sipproxy is disabled.