When you allow the Comment viewing options for a node_type then the comment_controls are displayed. When you change any of the dropdown and click save you expect that the values you selected there to be selected but actually they are not.
The problem is that you get the form with : drupal_get_form('comment_controls', $mode, $order, $comments_per_page). That is just fine but you forget that drupal_get_form adds $form_values always as first argument to the form so the function for the form should be : function comment_controls($form_values, $mode = COMMENT_MODE_THREADED_EXPANDED, $order = COMMENT_ORDER_NEWEST_FIRST, $comments_per_page = 50) and not without the $form_values as first argument. Hope that you will fix this in future releases.
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Comment #1
vflirt commentedI see that this is fixed in drupal 6.9 :)