Give the gift of Drupal. All merchandise is 50% off through 2016.
I had this issue with the Biblio module: it defines $form['body_field']['body'] with weight 19, and $form['body_field']['format'] with weight 20.
Then after better_formats_form_alter() has run, the format fieldset displays above the body field, because it resets the weight to 1.
This patch has been made against 6.x-1.2, but a quick look at the CVS repo tells me it should apply against 2.x-dev too...