diff --git a/src/aare/gui/main_window.py b/src/aare/gui/main_window.py
index daa6d885..94ac0c2d 100644
--- a/src/aare/gui/main_window.py
+++ b/src/aare/gui/main_window.py
@@ -745,9 +745,6 @@ class MainWindow(QMainWindow):
             self.automation_progress_panel.set_running
         )
         self.job_list_panel.automation_running_changed.connect(self._on_automation_running_changed)
-        self.job_list_panel.automation_running_changed.connect(
-            self.data_collection.set_automation_running
-        )
 
         self.automation_progress_panel.set_samples_in_queue(
             len(self.job_list_panel.table_model.samples)
@@ -1027,6 +1024,7 @@ class MainWindow(QMainWindow):
         )
 
         self.job_list_panel.auto_scan.connect(self.daq.automated_scan)
+        self.job_list_panel.auto_scan.connect(self.data_collection.auto_scan_started)
 
         self.job_list_panel.unmount.connect(self.daq.unmount)
         self.job_list_panel.unmount_then_park_and_dry.connect(self.daq.unmount_then_park_and_dry)
@@ -1151,6 +1149,7 @@ class MainWindow(QMainWindow):
 
         self.daq.automated_scan_done.connect(self.job_list_panel.automated_scan_done)
         self.daq.automated_scan_done.connect(self._mark_scan_result)
+        self.daq.automated_scan_done.connect(self.data_collection.auto_scan_finished)
         self.daq.automation_critical_failure.connect(self._on_automation_critical_failure)
         self.daq.manual_collection_critical_failure.connect(
             self._on_manual_collection_critical_failure
diff --git a/src/aare/gui/panels/data_collection_settings.py b/src/aare/gui/panels/data_collection_settings.py
index 184b1030..8f7d982d 100644
--- a/src/aare/gui/panels/data_collection_settings.py
+++ b/src/aare/gui/panels/data_collection_settings.py
@@ -197,7 +197,7 @@ class DataCollectionSettings(QFrame):
         self._status_seen = False
         # Set on mount, fired once the hw lock frees (see _track_sample).
         self._center_after_mount_pending = False
-        self._automation_running = False
+        self._auto_scans_in_flight = 0
 
         self._tab_bar.currentChanged.connect(self._stack.setCurrentIndex)
         self._tab_bar.currentChanged.connect(self._on_tab_changed)
@@ -261,7 +261,7 @@ class DataCollectionSettings(QFrame):
             self._center_after_mount_pending = (
                 self._status_seen
                 and self.auto_center_after_mount.isChecked()
-                and not self._automation_running
+                and not self._auto_scans_in_flight
             )
         self._status_seen = True
         # The server publishes the new sample while the mount still holds the
@@ -273,14 +273,20 @@ class DataCollectionSettings(QFrame):
             # main_window) instead of a second signal path.
             self.find_tip.click()
 
-    @Slot(bool)
-    def set_automation_running(self, running: bool):
-        # Queue automation centers each sample itself and frees the hw lock
-        # between samples; a GUI centering in that gap could steal the lock
-        # from the next /scan/auto and stop the queue.
-        self._automation_running = running
-        if running:
-            self._center_after_mount_pending = False
+    # Queue automation centers each sample itself and frees the hw lock
+    # between samples; a GUI centering in that gap could steal the lock from
+    # the next /scan/auto. Tracks the request, not the queue's running flag,
+    # because Pause flips that flag while the current sample is still running.
+    # A counter, since the queue sends the next scan before the settings panel
+    # sees the previous one's done signal.
+    @Slot()
+    def auto_scan_started(self):
+        self._auto_scans_in_flight += 1
+        self._center_after_mount_pending = False
+
+    @Slot()
+    def auto_scan_finished(self):
+        self._auto_scans_in_flight = max(0, self._auto_scans_in_flight - 1)
 
     @Slot(int)
     def _on_tab_changed(self, idx: int):
diff --git a/tests/unit/gui/test_data_collection_settings.py b/tests/unit/gui/test_data_collection_settings.py
index 307c228d..0020a565 100644
--- a/tests/unit/gui/test_data_collection_settings.py
+++ b/tests/unit/gui/test_data_collection_settings.py
@@ -376,7 +376,7 @@ def test_auto_center_waits_for_mount_to_release_hw_lock(settings_panel):
     assert len(clicks) == 1
 
 
-def test_auto_center_skipped_during_queue_automation(settings_panel):
+def test_auto_center_skipped_while_auto_scan_in_flight(settings_panel):
     # Automation centers itself and frees the lock between samples; a GUI
     # centering there could steal the lock from the next /scan/auto.
     clicks = []
@@ -384,14 +384,25 @@ def test_auto_center_skipped_during_queue_automation(settings_panel):
     settings_panel.auto_center_after_mount.setChecked(True)
     settings_panel._track_sample(1)
 
-    settings_panel.set_automation_running(True)
+    # Queue sends the next scan before the settings panel sees the previous one
+    # finish (signal order in main_window): must still count as in flight.
+    settings_panel.auto_scan_started()
+    settings_panel.auto_scan_started()
+    settings_panel.auto_scan_finished()
     settings_panel._track_sample(2, busy=True)
     settings_panel._track_sample(2, busy=False)
     assert not clicks
 
-    settings_panel.set_automation_running(False)
+    # Pause mid-sample: the current scan still runs to completion, so no
+    # centering until its request is done and a later manual mount happens.
     settings_panel._track_sample(3, busy=True)
+    settings_panel.auto_scan_finished()
     settings_panel._track_sample(3, busy=False)
+    assert not clicks
+
+    settings_panel._track_sample(None)
+    settings_panel._track_sample(4, busy=True)
+    settings_panel._track_sample(4, busy=False)
     assert len(clicks) == 1