The last couple of days I have been converting my oldest site, whitelakeworld.com, to Drupal 7.12. I came across the problem of not being able to access a password protected directory in the web root outside of my Drupal install. I had the same problem when I converted this site to Drupal a while back and let it stump me.
On both sites I have a script that runs from cron to update a section of the site devoted to affiliate products. It simply takes a datafeed file and uses it to update the database.