I use Calibre to convert my pdf documents and sync them to both my Kindle and my phone. This way I don't have to think about where I'm reading them (I have the latest version of Calibre installed). I'm wondering if that's what is somehow synchronizing the books.
Susan, do you remember where you read about this Calibre "feature"?
<Edit>I found the post that showed me how to fetch annotations in Calibre:
However, I'm still not sure if that's what triggered this. I think personal file sync started happening after the 3.1 upgrade. I am not putting anything in the ISBN number field.