OK I've done the captureurl option using the command line utils (see cmd below)
for my site and hit the httrack's disclaimer of the built-in method not
working for everything. However, I am curious if there is any other method to
get at pages that require authentication?
Some site info:

The content (after logging in) resides on two servers. One is a ASP web box
and the other uses the WEBGUI CMS system. 

The landing page (on the asp box) is not password protected and does not
require authentication to view it but does requires cookies and javascript to
authenticate your credentials. Many other links on the landing page are also
freely viewable and they are captured. The only time you enter the
"authenticated zone" is after you hit the submit button which then sends you
to the other server's pages to start off with. From there you can dance back
and forth between the two servers depending on what you select to view.

*****End Site Info Blurb*****

Now one idea I have is if I were to create a new site but already has the
authentication information hard coded in a single landing page that then sends
you to the authenticated zone just as if you had clicked submit on the
original landing page. Has anyone tried that? Does/Would it work? Link of site
embedded in command linke info below.

**** command line info ****
 httrack <http://my.comtrol.com> -O "/sitemirrors/my_comtrol_com"
"+support.comtrol.com/*" -m5000000,1000000 -M1000000000 -A1000000 -c1 -T30 -R2
-J10 -%l "en" -n
***************************

Any pointers/ideas and/or methods used to get around the disclaimer are much
appreciated.

Thanks!