I've also had syncing problems. I recently did a soft factory reset from the menu and I've only copied a fraction of my books back onto the device, and now sync is working and fast.
I've been adding handfuls of books a day (weeding out ones I don't really need on the device all the time), and so far the problem hasn't come back.
I'm wondering if it is just dumping a huge number of books on it all at once that makes sync fail, or if there's one specific book (which I haven't hit yet) that causes it, or if it is the total number of books (or shelves) that causes it.
In
this message @davidfor suggested conflicting case in shelf names causes it, but his solution didn't completely work for me, but I haven't been able to verify why.