hmmm, that sounds like a bug either with the sync tool, or the bookstore, rather than the kobo itself...
I've read 10-15 books so far (all drm-free, either from Baen or the like, or where I grabbed the book online because I already have a tree-ware copy), and haven't had any problems at all. I guess I also don't use the sync tool, but rather copy files to the kobo directly...
There is also a way to reset the status of all of the books by editing the sql database on the kobo - I had randomly opened a bunch of books to look at the formatting, and didn't want to close all of them manually, so it was infinitely quicker to do it that way. Info can be found somewhere in the forums on how to do this, its easy enough.
Not that I wouldn't love to see a "Close book" option in the next firmware release, of course
