Did you try reloading the books through Calibre? It appears there may be a problem with Calibre and sync at the moment--though mostly we have seen books going from I'm Reading into Books and losing bookmarks. Tim Legge, who does the Calibre drivers, is looking into it.
That being said, the 1.7.3 version of the Kobo desktop is really a problem. The replacement is in outside beta testing.
Older versions of Calibre are here:
http://sourceforge.net/projects/calibre/files/ You can go back a version or two and see if that fixes anything