Hmm, I would call it a bug...
I select some files, invoke File Organizer with "add to library" checked and only some of the files are added to the library. There have been cases (specially when an album has lots of tracks) where I haven't noticed the "missing" library files until some time later.
Either add all the files or none of them. And IMHO adding all the files is the correct option, as it's the action chosen by the user.
Right now, I have "add to library" unchecked, as the behavior is not reliable.
Note that for most users this does not happen, as Inbox files aren't usually in the same place as library files. It just happens that I'm rebuilding my library "in place".
EDIT: oops, never mind - while writing my answer went to coffee and didn't see your answer until after I posted mine. Thanks for the change.