Empty lines in index.php file
If your index.php file is different from the default one, then it has been changed from somebody.
Updates to modules don't alter the content of that file. If there is a module that tries to alter the content of index.php, that is not the correct behavior for that module.

I would check that the permissions of the system user used to run the server, and PHP, don't allow it to alter any file contained in the Drupal root directory, and in its sub-directories.

In Drupal 6, the content of index.php is the following one. It is 39-line long, it includes an empty line after drupal_page_footer();, and it doesn't have any closing tag (?&gt;).

&lt;?php

/**
 * @file
 * The PHP page that serves all page requests on a Drupal installation.
 *
 * The routines here dispatch control to the appropriate handler, which then
 * prints the appropriate page.
 *
 * All Drupal code is released under the GNU General Public License.
 * See COPYRIGHT.txt and LICENSE.txt.
 */

require_once './includes/bootstrap.inc';
drupal_bootstrap(DRUPAL_BOOTSTRAP_FULL);

$return = menu_execute_active_handler();

// Menu status constants are integers; page content is a string.
if (is_int($return)) {
  switch ($return) {
    case MENU_NOT_FOUND:
      drupal_not_found();
      break;
    case MENU_ACCESS_DENIED:
      drupal_access_denied();
      break;
    case MENU_SITE_OFFLINE:
      drupal_site_offline();
      break;
  }
}
elseif (isset($return)) {
  // Print any value (including an empty string) except NULL or undefined:
  print theme('page', $return);
}

drupal_page_footer();