swftools.module line 27

define('SWFTOOLS_DEFAULT_BG', url(drupal_get_path('module', 'swftools') . '/shared/swftools-default.jpg', array('absolute' => TRUE)));   // A generic image for use in certain contexts.

the problem is with calling url() before hook_init().
purl_url_outbound_alter() is called before purl_init(), therefore the purl_cache is empty at url rewrite, and the links on the page are not rewritten.