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pjm13,
The error is occurring during the email fetch--but not at the beginning where I would have expected. That's indicated by your report that some, but not all of the notification emails are being marked read.
Give what's happening, I wonder how full your mailbox is? FFF searches for all unread ('UNSEEN' in imap4) and fetches and looks through all of them for story URLs.
If you point it at your normal inbox and keep tons of old unread messages around, it might make a difference.
Or even tons of read messages--I have a dedicated inbox I use for update notifications and FFF is noticeably faster fetching from it when I've deleted everything from it.
I might be able to increase the connection timeout, but I'd like to see a debug log first; that should show how long it's taking.
Run Calibre in debug mode from the Calibre Preferences drop down.
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