diff --git a/toolkit/xre/nsAppRunner.cpp b/toolkit/xre/nsAppRunner.cpp
--- a/toolkit/xre/nsAppRunner.cpp
+++ b/toolkit/xre/nsAppRunner.cpp
@@ -3342,23 +3342,16 @@ XRE_main(int argc, char* argv[], const n
         }
         dirProvider.DoStartup();
 
         PRBool shuttingDown = PR_FALSE;
         appStartup->GetShuttingDown(&shuttingDown);
 
         nsCOMPtr<nsICommandLineRunner> cmdLine;
 
-#if defined(HAVE_DESKTOP_STARTUP_ID) && defined(MOZ_WIDGET_GTK2)
-        nsRefPtr<nsGTKToolkit> toolkit = GetGTKToolkit();
-        if (toolkit && !desktopStartupID.IsEmpty()) {
-          toolkit->SetDesktopStartupID(desktopStartupID);
-        }
-#endif
-
         nsCOMPtr<nsIFile> workingDir;
         rv = NS_GetSpecialDirectory(NS_OS_CURRENT_WORKING_DIR, getter_AddRefs(workingDir));
         NS_ENSURE_SUCCESS(rv, 1);
 
         if (!shuttingDown) {
           cmdLine = do_CreateInstance("@mozilla.org/toolkit/command-line;1");
           NS_ENSURE_TRUE(cmdLine, 1);
 
@@ -3376,16 +3369,23 @@ XRE_main(int argc, char* argv[], const n
 
           NS_TIMELINE_ENTER("appStartup->CreateHiddenWindow");
           rv = appStartup->CreateHiddenWindow();
           NS_TIMELINE_LEAVE("appStartup->CreateHiddenWindow");
           NS_ENSURE_SUCCESS(rv, 1);
 
           MOZ_SPLASHSCREEN_UPDATE(50);
 
+#if defined(HAVE_DESKTOP_STARTUP_ID) && defined(MOZ_WIDGET_GTK2)
+          nsRefPtr<nsGTKToolkit> toolkit = GetGTKToolkit();
+          if (toolkit && !desktopStartupID.IsEmpty()) {
+            toolkit->SetDesktopStartupID(desktopStartupID);
+          }
+#endif
+
           // Extension Compatibility Checking and Startup
           if (gAppData->flags & NS_XRE_ENABLE_EXTENSION_MANAGER) {
             nsCOMPtr<nsIExtensionManager> em(do_GetService("@mozilla.org/extensions/manager;1"));
             NS_ENSURE_TRUE(em, 1);
 
             if (upgraded) {
               rv = em->CheckForMismatches(&needsRestart);
               if (NS_FAILED(rv)) {