Hook footer is not allowed to add javascript to headers

From API: http://api.drupal.org/api/function/hook_footer/6

Insert closing HTML.

This hook enables modules to insert HTML just before the \ closing tag of web pages. This is useful for adding JavaScript code to the footer and for outputting debug information. It is not possible to add JavaScript to the header at this point, and developers wishing to do so should use hook_init() instead.

So this ...

/**
 *  Invoke the plugin on any page listed from the configuration page.
 *  Code swiped from block_list
 */
function jquery_media_footer() {
  $path = drupal_get_path_alias($_GET['q']);
  $regexp = '/^('. preg_replace(array('/(\r\n?|\n)/', '/\\\\\*/', '/(^|\|)\\\\<front\\\\>($|\|)/'), array('|', '.*', '\1'. preg_quote(variable_get('site_frontpage', 'node'), '/') .'\2'), preg_quote(variable_get('jquery_media_pages', ''), '/')) .')$/';
  // Compare with the internal and path alias (if any).
  $page_match = preg_match($regexp, $path);
  if ($path != $_GET['q']) {
    $page_match = $page_match || preg_match($regexp, $_GET['q']);
  }
  if ($page_match) {
    jquery_media_add();
  }
}

should be...

/**
 *  Invoke the plugin on any page listed from the configuration page.
 *  Code swiped from block_list
 */
function jquery_media_init() {
  $path = drupal_get_path_alias($_GET['q']);
  $regexp = '/^('. preg_replace(array('/(\r\n?|\n)/', '/\\\\\*/', '/(^|\|)\\\\<front\\\\>($|\|)/'), array('|', '.*', '\1'. preg_quote(variable_get('site_frontpage', 'node'), '/') .'\2'), preg_quote(variable_get('jquery_media_pages', ''), '/')) .')$/';
  // Compare with the internal and path alias (if any).
  $page_match = preg_match($regexp, $path);
  if ($path != $_GET['q']) {
    $page_match = $page_match || preg_match($regexp, $_GET['q']);
  }
  if ($page_match) {
    jquery_media_add();
  }
}