diff --git a/libs/ardour/session_click.cc b/libs/ardour/session_click.cc
index c31636f7fa..3a0d50ff65 100644
--- a/libs/ardour/session_click.cc
+++ b/libs/ardour/session_click.cc
@@ -174,6 +174,9 @@ Session::run_click (samplepos_t start, samplepos_t nframes)
 	/* given a large output latency, `start' can be offset by by > 1 cycle.
 	 * and needs to be mapped back into the loop-range */
 	Location* loop_location = get_play_loop () ? locations()->auto_loop_location () : NULL;
+	if (_count_in_samples > 0) {
+		loop_location = NULL;
+	}
 	bool crossloop = false;
 	samplecnt_t span = nframes;
 	if (loop_location) {
@@ -216,6 +219,9 @@ Session::run_click (samplepos_t start, samplepos_t nframes)
 			 * clicks at loop-start into account */
 			const samplepos_t loop_start = loop_location->start ();
 			internal_offset = clk->start - loop_start + span;
+		} else if (_count_in_samples > 0) {
+			++i;
+			continue;
 		} else {
 			/* this can happen when locating
 			 * with an active click */
diff --git a/libs/ardour/session_transport.cc b/libs/ardour/session_transport.cc
index 7abf43b062..4e8a872b68 100644
--- a/libs/ardour/session_transport.cc
+++ b/libs/ardour/session_transport.cc
@@ -648,6 +648,8 @@ Session::start_transport ()
 			int clickbeat = 0;
 			samplepos_t cf = _transport_sample - _count_in_samples;
 			samplecnt_t offset = _click_io->connected_latency (true);
+			clear_clicks ();
+			_clicks_cleared = cf;
 			while (cf < _transport_sample + offset) {
 				add_click (cf, clickbeat == 0);
 				cf += dt;