System: Fix frame advance+runahead stepping 2 frames

src/core/system.cpp

@@ -2192,9 +2192,11 @@ void System::FrameDone()
   {
     Host::PumpMessagesOnCPUThread();
     InputManager::PollSources();
-    CheckForAndExitExecution();
   }
 
+  // Frame step can still trigger exit
+  CheckForAndExitExecution();
+
   // Update input OSD if we're running
   if (g_settings.display_show_inputs)
     ImGuiManager::UpdateInputOverlay();