As [Marc][1] had originally written, the user prefs were stored inside a new table in `weblogData.prefs`. For a number of reasons, including forward compatibility we had decided to change this so that the prefs are now stored in a new table at `MarkdownData.prefs.user.Markdown`.
The default prefs are still at `MarkdownData.docs.prefs`. So far there is no breakage. If something’s not working let me know.
If you are a current user of the tool your current prefs should be placed into the new location automatically.
[1]: http://radio.weblogs.com/0104487/