Just Write is a webapp that allows you to express your ideas and musings in a comfortable, distraction-free environment. Just Write specifically caters towards writing for the web, providing markdown support and "export to HTML" functionality.
If I have three documents, the first and last being very short, but the middle having a large amount of text. I then work on the middle document, and hit save (or let it autosave). The last document gets overwritten with a duplicate of the middle document which I am working on.
I'm guessing that this is some kind of session thing, whereby it is getting confused as to which document it is saving?