diff --git a/libs/ardour/globals.cc b/libs/ardour/globals.cc
index afcaa4dfcd..fd70aa34d7 100644
--- a/libs/ardour/globals.cc
+++ b/libs/ardour/globals.cc
@@ -341,8 +341,6 @@ ARDOUR::init_post_engine ()
 	if ((node = Config->control_protocol_state()) != 0) {
 		ControlProtocolManager::instance().set_state (*node, Stateful::loading_state_version);
 	}
-
-	MIDI::Manager::instance()->set_port_states (Config->midi_port_states ());
 }
 
 int
diff --git a/libs/ardour/session.cc b/libs/ardour/session.cc
index 040210676b..6d3a73343a 100644
--- a/libs/ardour/session.cc
+++ b/libs/ardour/session.cc
@@ -63,6 +63,7 @@
 #include "ardour/butler.h"
 #include "ardour/click.h"
 #include "ardour/configuration.h"
+#include "ardour/control_protocol_manager.h"
 #include "ardour/crossfade.h"
 #include "ardour/cycle_timer.h"
 #include "ardour/data_type.h"
@@ -517,6 +518,17 @@ Session::when_engine_running ()
 
 	BootMessage (_("Setup signal flow and plugins"));
 
+	ControlProtocolManager::instance().set_session (this);
+
+	/* This must be done after the ControlProtocolManager set_session above,
+	   as it will set states for ports which the ControlProtocolManager creates.
+	*/
+	MIDI::Manager::instance()->set_port_states (Config->midi_port_states ());
+
+	/* And this must be done after the MIDI::Manager::set_port_states as
+	 * it will try to make connections whose details are loaded by set_port_states.
+	 */
+
 	hookup_io ();
 
 	if (_is_new && !no_auto_connect()) {
diff --git a/libs/ardour/session_state.cc b/libs/ardour/session_state.cc
index 0c4a1a767b..00523ad933 100644
--- a/libs/ardour/session_state.cc
+++ b/libs/ardour/session_state.cc
@@ -368,10 +368,6 @@ Session::second_stage_init ()
 
 	/* initial program change will be delivered later; see ::config_changed() */
 
-	BootMessage (_("Reset Control Protocols"));
-
-	ControlProtocolManager::instance().set_session (this);
-
 	_state_of_the_state = Clean;
 
 	Port::set_connecting_blocked (false);