There has been patch apparently that changes the way connections are made. I have friend that i play often but occasionally we can't join each others games. Sometimes we can fix it by booting the faf client or booting one of the computers. To the best of our knowledge, this happens randomly. After a recent patch, we occasionally get the note about faf using a proxy, but not always.
After a patch, we have a new symptom that we have never seen before. Before the patch, once we got a game going, it would work perfectly and we even could play several games afterwards with no problems. Now, we can lose the connection during the game. Both players see the same "quiet for" window and once we exit the game, we've lost our connection to faf as well. Both of us. It says "the remote host has closed the connection". I never have problems with anyone else but this one friend, i might add.