Which command are you trying... create menu or create menu item? Both work for me as advertised and neither destroys the File menu. Please post your script again.
... Perhaps this is what you are seeing...
menu -gwmpv; // select all menu bars menu 1 (Test); // add Test menu at 1st position
Click on any window or the Refresh button. The menu bar looks like this...
Test File Edit ...
The Test menu has no menu items and therefore does not expand when you select it with the mouse. Other menus also do not expand if you just pass the mouse cursor over them but clicking on the menu name will force them to expand.