--- old/src/macosx/classes/com/apple/eawt/_AppEventHandler.java	2012-03-23 20:29:13.000000000 +0400
+++ new/src/macosx/classes/com/apple/eawt/_AppEventHandler.java	2012-03-23 20:29:13.000000000 +0400
@@ -157,7 +157,10 @@
                 }
             });
         } 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);
         }
     }