Mag,
Your menu is still there but has probably scrolled out of view (I assume you're on a Mac, otherwise you'd see it.) This is how menus work on Mac. When you want the stack to scroll the menu area back into view so you can edit or see it, do as Klaus suggested and set the editmenus of the stack to true in the message box:
set the editmenus of this stack to true
Menu Builder is reliable for the most part. I generally use it to set up the menu structure and the skeleton scripts. After that I do any other editing in the property inspector. But you can continue to use Menu Builder to edit if you make sure you are working on the correct menu group. You really don't want to assign two groups as the menu in a stack, that will confuse things. Click the Edit button and choose the existing menu group to edit it. You can toggle the visibility of the group from there too, uncheck the button that sets the group as the stack menubar. Remember to set it back again later.
I have a tutorial about how menus work in LiveCode. Once you understand it the scrolling makes more sense:
http://www.hyperactivesw.com/mctutorial ... Menus.html