Please use attached project and try the following:

1. Run the application and move toolWindow3 from right to the bottom panel.
2. Hide toolWindow3 by 'Toggle' menu item or just close it.
3. Save the layout pressing 'Save' menu item.
4. Close the application and run it again.
5. Restore layout using 'Init' menu item.
6. Press 'Toggle' menu item to show toolWindow3. 

Workaround:
Make the window visible before loading the layout.