When you set up custom menus you can define the modes it applies to (Browse, Find, Preview). As you cannot select Layout mode it follows that custom menus do not apply to that mode; this is logical, as Layout mode has its own menu (eg. Layout and Arrange added, Records removed, etc). In the same way, Manage Scripts has its own menu with irrelevant menus removed.
Ie. This is not a bug. Generally only a full access account accesses these environments....