diff --git a/libs/ardour/ardour/location.h b/libs/ardour/ardour/location.h
index 826834b208..0db7e705e2 100644
--- a/libs/ardour/ardour/location.h
+++ b/libs/ardour/ardour/location.h
@@ -212,6 +212,8 @@ public:
 	bool clear_xrun_markers ();
 	bool clear_ranges ();
 
+	void clear_cue_markers (samplepos_t start, samplepos_t end);
+
 	void ripple (timepos_t const & at, timecnt_t const & distance, bool include_locked, bool notify);
 
 	XMLNode& get_state (void);
diff --git a/libs/ardour/location.cc b/libs/ardour/location.cc
index e6313d3ebb..b73f0bf2ad 100644
--- a/libs/ardour/location.cc
+++ b/libs/ardour/location.cc
@@ -1622,3 +1622,54 @@ Locations::ripple (timepos_t const & at, timecnt_t const & distance, bool includ
 		changed(); /* EMIT SIGNAL */
 	}
 }
+
+void
+Locations::clear_cue_markers (samplepos_t start, samplepos_t end)
+{
+	TempoMap::SharedPtr tmap (TempoMap::use());
+	Temporal::Beats sb;
+	Temporal::Beats eb;
+	bool have_beats = false;
+	vector<Location*> r;
+
+
+	{
+		Glib::Threads::RWLock::WriterLock lm (_lock);
+
+		for (LocationList::iterator i = locations.begin(); i != locations.end(); ) {
+
+			if ((*i)->is_cue_marker()) {
+				Location* l (*i);
+
+				if (l->start().time_domain() == AudioTime) {
+					samplepos_t when = l->start().samples();
+					if (when >= start && when < end) {
+						i = locations.erase (i);
+						r.push_back (l);
+						continue;
+					}
+				} else {
+					if (!have_beats) {
+						sb = tmap->quarters_at (timepos_t (start));
+						eb = tmap->quarters_at (timepos_t (end));
+						have_beats = true;
+					}
+
+					Temporal::Beats when = l->start().beats();
+					if (when >= sb && when < eb) {
+						r.push_back (l);
+						i = locations.erase (i);
+						continue;
+					}
+				}
+			}
+
+			++i;
+		}
+	} /* end lock scope */
+
+	for (auto & l : r) {
+		removed (l); /* EMIT SIGNAL */
+		delete l;
+	}
+}
diff --git a/libs/ardour/session_transport.cc b/libs/ardour/session_transport.cc
index dad51ea53c..d3452a2b5a 100644
--- a/libs/ardour/session_transport.cc
+++ b/libs/ardour/session_transport.cc
@@ -1355,6 +1355,11 @@ Session::non_realtime_stop (bool abort, int on_entry, bool& finished)
 		auditioner->cancel_audition ();
 	}
 
+	/* This must be called while _transport_sample still reflects where we stopped
+	 */
+
+	flush_cue_recording ();
+
 	if (did_record) {
 		begin_reversible_command (Operations::capture);
 		_have_captured = true;
@@ -1476,7 +1481,6 @@ Session::non_realtime_stop (bool abort, int on_entry, bool& finished)
 
 	clear_clicks();
 	unset_preroll_record_trim ();
-	flush_cue_recording ();
 
 	/* do this before seeking, because otherwise the tracks will do the wrong thing in seamless loop mode.
 	*/
@@ -2084,9 +2088,15 @@ Session::actual_speed() const
 void
 Session::flush_cue_recording ()
 {
+	if (!TriggerBox::cue_records.read_space()) {
+		return;
+	}
+
 	CueRecord cr;
 	TempoMap::SharedPtr tmap (TempoMap::use());
 
+	_locations->clear_cue_markers (_last_roll_location, _transport_sample);
+
 	while (TriggerBox::cue_records.read (&cr, 1) == 1) {
 		BBT_Time bbt = tmap->bbt_at (timepos_t (cr.when));
 		bbt = bbt.round_up_to_bar ();