After you delete a window, you must also manually delete its associated modelPanel using the deleteUI command. The model panel is not deleted automatically when the window is deleted.
For example:
// Create a window called myWindow window -wh 640 480 myWindow; paneLayout; // Save modelPanel as a string named panel string $panel = `modelPanel`; showWindow myWindow; // Set a script job so that when myWindow is deleted, modelPanel is also deleted scriptJob -uiDeleted "myWindow" ("{ deleteUI -panel " + $panel + "; }");