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.
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 No External Pages so I know where the mirror ends. I
always run with broswer ID=msie6 as some sites don't like a HTT one. I always
run with Attempt to detect all links.

> This is the final script that I ran, I tried a few
> other ways, including changing the browser ID to the
> default that httrack provides.
Not according to what you posted below

> (winhttrack
> -qi%e0C2%PnX0s2u1k%s%uN0%I0p3DaK0c8R2H0%kf2A25000%f#
> f -F "HTTrack Website Copier/3.0x (offline browser;
> web mirror utility)" -%F  -%l "en, en, *"
> <http://www.vulnerabilityassessment.co.uk/> -O1
> "C:\My\Dir\VulnAssessment_uk" +*.png +*.gif +*.jpg
> +*.css +*.js +.pdf +*.zip +*.tar +*.tgz +*.gz +*.rar
> +*.z +*.exe -ad.doubleclick.net/* )

Drop the filters, you already used the near flag, so they do nothing.

> Everything appears to be in the correct directories,
> including the .js files that I can see when
> inspecting elements of the original we page using
> Safari.
> I have Java installed and allowed. I am using IE8,
> Chrome and Iron to view the downloaded site with the
> same results.

You state NO PROBLEM, so we can't even guess a solution.