[Oops, sorry for the previous empty message]

> but when I examine the source for the 
> category listing page, httrack has left the links to the 
> documents themselves which also live in the CMS alone, 
> rather than traversing and downloading the documents... ?> I have played
with filters until I am blue in the face 
and 
> have set --assume .cgi=text/html.

You certainly mean: 
--assume cgi=text/html

This will speed up the transfers, but not affect the number 
of links downloaded.

> My starting url is; my-intranet-node/simpleBrowse.htm 
> The URL's that are not being parsed look like;
> <http://my-intranet-node/cgi-bin/cms/cms.cgi>?
This is weird, because these links should be downloaded, if 
not inside complex javascripting.

Did you try to use filters (set options/scan rules) ? 
Like +my-intranet-node/cgi-bin/cms/cms.cgi?*