src/macosx/classes/com/apple/eawt/_AppEventHandler.java

@@ -155,11 +155,14 @@
                         frame.dispatchEvent(new WindowEvent(frame, WindowEvent.WINDOW_CLOSING));
                     }
                 }
             });
         } finally {
-            nativeReplyToAppShouldTerminate(true);
+            // Either we've just called System.exit(), or the app will call
+            // it when processing a WINDOW_CLOSING event. Either way, we reply
+            // to Cocoa that we don't want to exit the event loop yet.
+            nativeReplyToAppShouldTerminate(false);
         }
     }
 
     /*
      * callbacks from native delegate