I also had this problem. I was pleased that everything worked flawlessly with Calibre, Stanza and my iPod. Then today, without warning, and without making any changes, I could no longer hook up to the server.
I spent the better part of the day going through the manuals, FAQs, and forums, and tried everything I ran across, to no avail. I was thoroughly disgusted and gave up, restoring all settings, port changes, etc., to what they were in the first place. Two hours later, it simply started working again.