Plugins can inject items into settings menus (the core administration block) using the "extend_settings_navigation" hook function. In Clean, this shows up in the "Administration" menu for the page in the tree structure. In Boost, this generally shows up in the main admin page structure (/admin/search.php) or in the settings dropdown for a specific element (e.g. course or module).
However, in some case, menu items that have been added to other areas don't show up anywhere in Boost even though they are accessible in Clean. They can be forced by adding the "administration" block to a page in question though.
For example, using a local plugin called "metadata", I have added a new setting for course module instances. When I access a course module, I can see an entry for "Instance metadata" in the course module's settings menu (see attachment 1). Likewise this shows up in the administration block (see attachment 2).
But if I add a new setting for cohorts (or groups), I can only access the new entry from the administration block (see attachment 3). Boost does not add the menu entry to any structure (see attachment 4).
Boost should provide a way for access to these entries injected using the "extend" hook.