Submitting this as an issue as per sepeck's request on this thread http://drupal.org/node/62746. Not sure if it's a bug or a feature request though.
We ran into it when we moved our forums over from phpbb - we disallowed signatures on phpbb, but there's no setting to turn them off in drupal. We're using a modified flatforum template, and took out the $sig line in node-forum.tpl.php which prints signatures dynamically - but they were still appearing. The only way to remove signatures from comments for us was to comment out the relevant code in comment.module (as described on that thread):
$form['comment_filter']['comment'] = array('#type' => 'textarea', '#title' => t('Comment'), '#rows' => 15, '#default_value' => $edit['comment']/* ? $edit['comment'] : $user->signature*/, '#required' => TRUE);
We didn't have an issue with duplicate signatures as described in the discussion, we just wanted to get rid of them altogether. Since everything else can be switched on or off in the theme though, it seems odd that comments are pre-loaded into the text area for comments. This also means that if a user changes their signature, the old one will still appear in all their old posts, it adds to the amount of data in the comment table since the text is duplicated every time the user comments, and it makes it difficult for admins to control display.
Since both flatforum and (apparently) the signature module allow for dynamic display of signatures, it would make sense for either their functionality to be included into core, or for the pre-inclusion of signatures to be disabled in comment.module and then if people want signatures displayed, they could use one of the contrib modules.
Hope this is alright for an issue posting - my first one...