Before you sync, are the books listed in the desktop application the same books that are in "I'm Reading" on your Kobo WiFi (except for new purchases)? Do you, by any chance, share your account with someone else in your family who also is syncing? We are a multiple Kobo household but only one of us uses sync because of the issues that happen when people do not have the exact same books on the go, or are reading the same book, but have different points bookmarked.
I would recommend that until Borders releases the new desktop application for you, that you use WiFi if you can. The sync is better than with the older desktop software. The new desktop software is much improved.
I'm betting that you know this already, but you can only sync to one bookstore--choose Borders or choose Kobobooks, and download ePUB files for the bookstore you don't sync with.
Last edited by taming; 01-03-2011 at 02:34 AM.