I assume you mean the automatic import from a directory setting.
I occasionally have issues with it not importing books that way. I've found the following possible reasons:
- Calibre doesn't recognize it as a book (wrong file type? file type not in the supported list?) Might be able to rename the file to the correct extension or change a checkbox in calibre settings somewhere. (can't remember where I saw that off the top of my head)
- The file has the wrong permissions; not sure why this is a problem, but it is. It will import the book immediately after you make it world readable.
- The file has an old date. In linux, touching the file will cause it to be imported immediately.