Hello webcat.
As it turns out, the reason why I was unable to spider the .htaccess protected directory was not the .htaccess protection at all. As long as you write your url to be spidered like:
http://username:password@www.mydomain.com/....
or
https://username:password@secure.mydomain.com/....
it should work. The problem that I had was that the server would go into a loop it couldn't get out of. I am using php pages that use different checking mechanisms and redirects, and it worked perfectly in a browser, but it sent PhpDig into a neverending loop. So, if you are using php pages like discribed above you may want to try the fix that Charter posted as a download a bit higher up in the threads.
Hope that this will work for you.
Mr. L