> you did filter out the log-out url?
With http-auth there is no log-out possible, you can only end the session
(close browser) or log-in with other user:pass

The problem is that httrack doesn't log-in!

httrack user:pass@some.site/index.htm
will perfectly work until index.htm already exists locally. if index.htm
exists, the local version will be used and the links in it followed. These
links don't contain the user:pass part (some.site/linked.htm and not
user:pass@some.site/linked.htm) and therefore no authentication happens and
linked.htm gets a 401 error.

This is the same as if you try some.site/linked.htm in your browser and press
cancel when asked for user:pass - that can't work.