I read through and searched the forums about javascript and attempted the
different techniques, no joy.
I have used httrack in the past in Windows and Linux and have always had
success.
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.

From my log file:
HTTrack3.46+htsswf+htsjava launched on Mon, 17 Dec 2012 13:35:28 at
<http://www.vulnerabilityassessment.co.uk/> +*.png +*.gif +*.jpg +*.css +*.js
+.pdf +*.zip +*.tar +*.tgz +*.gz +*.rar +*.z +*.exe -ad.doubleclick.net/*

(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/* )

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.

I am not sure that is shows here but I checked the boxes for files that are
near and to parse java files.