Odgar, on calibre did you turn on the 'wireless device service' or the 'content manager'? I am betting the initial sync was just checking what you had stored on your iPad. I too didn't realize at the beginning your books or even a catalog are *not* automatically transferred.
Using iOS and the Mac applications I turned on the wireless device service calibre and setup CC as a wireless device and (after turning off my cellular connection and VPNs) highlighted my entire library, right clicked and instructed to send to the main memory. After waiting a few minutes on the first book they are transferring.
Not sure how sync'ing differs between using as a content server or wireless device, or even how to store a catalog on my iPhone as opposed to my library. My goal was to move my books to my phone and be able to use calibre super powers to manage my collection without needing my PC. Having used the app for all of 15 minutes, that has been where my research has been focused.
I hope you found your solution, or at least stick around the MobileReads community as we figure this sh*t out :-)
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