If you look at the tools >> Start Up options, you'll see that these are what you are setting programmatically. As such, they are read and acted upon at startup. If I want to set these sorts of things I tend to set them on the close event of my switchboard, anticipating what I will want them set to the next time it is opened (I use a vbYesNo message box so I have the option of setting it as I want). It is a pain during your development of this feature but it works fine once you have finished - I now just select yes if I know I am about to create an mde for distribution, other wise no.
So I change the properties of the form which is open to Modal.
Then I desactivate the shortcut menus. So only when the user press the special button, then he/she can "touch" the toolbar, he cannot use the shortcut menu, but it is ok, he/she can manage with the menu.