I've had sync issues with my iPad and iPhone, and they haven't gone away with the latest firmware update. I have pretty much the exact same problem the OP described--the Touch recognizes when I've been reading on another device, but it usually doesn't work the other way around.
One thing I've encountered that seems to help--but still is far from 100% reliable--is to exit a book on the iOS app before I exit the app itself. I.e. go back to my bookshelf. This seems to make it more likely that when I read on my touch, and then go back to the app, when I re-open the book it will be on the right page. But still, this is something that really needs to be fixed.
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