Yes, I have the same issue, sometimes.
I found that the automatically implemented Calibre-Server (in Stanza) rarely works. I added my library manually, then. And every time Stanza and Calibre can't find each other, I edit the Calibre-Link in Stanza, then save and it's visible.
I don't know if it's Calibre's or Stanza's fault ... but somehow it just doesn't work 100%.
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