I specified in the help file that items are only visible if they are in the room or being held. If you come across a container which holds an item you have to enter GET [item] FROM [container]. Function key F1 is pre-programmed for 'GET ALL FROM IT' so if you had examined the shelf and discovered that it held a book, hitting F1 [RETURN] would have got the book. Hope this helps.
If you have actions which are commonly used it's helpful to define your own function keys using the command DEFINE.