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wysiwyg_filter.module the function
passes the settings to the TinyMCE module. Passing over the settings breaks TinyMCE formatting (e.g. all inline styles are stripped off - altough the directive @[style] is set for the WYSIWYG filter).
Additionally, the Drupal way of filtering is doing it while the content is viewed and not when it's stored. Altough I think that it's valid to do such stuff in TinyMCE it may not be a good idea for a filter to do such stuff because developers won't expect to do it ?