diff --git a/src/Acquisition/FolderInputSystem.java b/src/Acquisition/FolderInputSystem.java
index b8e80f37..c8c2d872 100644
--- a/src/Acquisition/FolderInputSystem.java
+++ b/src/Acquisition/FolderInputSystem.java
@@ -690,7 +690,7 @@ public class FolderInputSystem extends FileInputSystem implements PamSettings, D
 		}
 		if (currentFile < allFiles.size()) {
 			// only restart if the file ended - not if it stopped
-			if (getStreamStatus() == STREAM_ENDED) {
+			if (getStreamStatus() == STREAM_ENDED && PamController.getInstance().isManualStop() == false) {
 //				System.out.println(String.format("Start new file timer (file %d/%d)",currentFile+1,allFiles.size()));
 				newFileTimer.start();
 			}
diff --git a/src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/PairBearingLocaliser.java b/src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/PairBearingLocaliser.java
index d6908eca..59c166fd 100644
--- a/src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/PairBearingLocaliser.java
+++ b/src/Localiser/algorithms/timeDelayLocalisers/bearingLoc/PairBearingLocaliser.java
@@ -214,7 +214,7 @@ public class PairBearingLocaliser implements BearingLocaliser {
 	private boolean resetArray(long timeMillis){
 		
 		if (this.timeMillis!=timeMillis && currentArray.getHydrophoneLocator().isChangeable()){
-			System.out.println("Reset PairBearingLocaliser");
+//			System.out.println("Reset PairBearingLocaliser");
 			prepare(this.arrayElements,  timeMillis, this.timingError);
 			return true;
 		}
diff --git a/src/PamController/PamController.java b/src/PamController/PamController.java
index 54f7735f..c52905fd 100644
--- a/src/PamController/PamController.java
+++ b/src/PamController/PamController.java
@@ -1099,7 +1099,8 @@ public class PamController implements PamControllerInterface, PamSettings {
 	 * later in the AWT event queue. 
 	 */
 	public void startLater() {
-		SwingUtilities.invokeLater(new StartLater(true));
+//		SwingUtilities.invokeLater(new StartLater(true));
+		startLater(true);
 	}
 
 	public void startLater(boolean saveSettings) {
@@ -1173,6 +1174,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	@Override
 	public void manualStop() {
 		lastStartStopButton = BUTTON_STOP;
+		setManualStop(true);
 		pamStop();
 	}
 
@@ -1186,6 +1188,7 @@ public class PamController implements PamControllerInterface, PamSettings {
 	@Override
 	public boolean pamStart() {
 		//		Debug.println("PAMController: pamStart");
+		setManualStop(false);
 		return pamStart(true);
 	}