The easiest way to check whether the files are, in fact, in your library is to use the Computer node in MusicBee's left sidebar to locate them on the drive. Then right click on a file, go to Send To, and see if Music Library is an available option. If it's grayed out, they are in your library, you just can't see them for some reason (maybe they're not sorting where you expect?). If it's not, you can use that to send them to the library. You can also use drag & drop. (Also notice whether Inbox is grayed out instead of Music Library - in that case, they were added to MusicBee, but are in the Inbox rather than the Music Library section. You would still send them to the library the same way.)