1) Always post the ACTUAL command line used (or log file line two) so we know
what the site is, what ALL your settings are, etc.
2) Always post the URLs you're not getting and from what URL it is
referenced.
3) Always post anything USEFUL from the log file.
4) If you want everything use the near flag (get non-html files related) not
filters.
5) I always run with A) No External Pages so I know where the mirror ends.
With B) browser ID=msie6 as some sites don't like a HTT one. With C) Attempt
to detect all links (for JS/CSS.) With D) Timeout=60, retry=9 to avoid
temporary network interruptions from deleting files.

> I scraped this wiki help page
> This tree structure breaks once downloaded for

Did you use #4 so you got all the JS that implements the menu?