On startup calibre scans and adds all files in the auto add folder. As for why it fails to add sometimes, it is most likely a file locking issue as theducks theorized. You can try running calibre in debug mode and see if anything useful is reported when such a failure occurs.
Just by the way, if you want to add books to calibre across the network, the best way to do it is run the embedded content server and just use its UI to add/convert books as needed.
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