The latest version of Twitter Tools seems to be having problems maintaining the "Notify Twitter" checkbox on new posts, especially scheduled posts.
A scheduled post goes live but does not tweet. When I check the post in the admin, the checkbox is turned off.
Also, when I submit a new post to my site using XML-RPC the twitter checkbox is not checked by default (even though it should be based on the settings).
Others are experiencing this problem too per the discussion on Alex's post. I'm posting here since that's what Alex says to do. :)