> Protocol on it, again using v3.44-1), and it caught
> the link, however, when I then proceeded to try and
> download the site, it failed immediately.

Failed immediately says nothing - no mind readers here.
What failed, what does the log file say?
> (winhttrack
> -qwC2%Pns0u1%s%uN0%I0p3DaK0H0%kf2A25000%f#f -F
> "Mozilla/4.5 (compatible; HTTrack 3.0x; Windows 98)"

Some sites do not like the HTT browser ID. I only run using msie6