> Am trying to capture the entire site - which includes 
files 
> that are not currently pointed to by a link.
> How?
You can't - the HTTP protocol does not allow to "list" all 
files in a site (which would be meaningless, because of all 
dynamically generated pages)

> I have found files referenced by Frontpage includes are 
not 
> captured.

Err, right - but are they visible within the html pages? 
Remember that httrack can only capture the result of 
dynamic pages, NOT their original sources. (it is more 
a "snapshot" than a real copy)