The cron semaphore is probably locked. You could try calling [drupal_cron_cleanup()][1] from anywhere in your code (that doesn't happen to be invoked by cron) and that should unlock your cron semaphore variable.

If you have drush configured in Drupal 6 you could also try:

    $ drush vdel -y cron_semaphore


  [1]: http://api.drupal.org/api/drupal/includes--common.inc/function/drupal_cron_cleanup/7