When you publish a VI, most of the menu operations are not supported and until you can control and run the VI (if it's not already running), the only menu item you will see is operate. Once the VI is running under your control, a custom menu item will appear but application items like File, Edit, Tools, etc. will not because those sort of operations are not allowed remotely and should not be. You are free to create user items with the same names and write your own menu handler in the code.