> I am getting a regular broken link message in the log 
file. 
> However the paths work fine in a browser.
> Here are the lines:
> 09:51:14 Error:  "Not Found" (404) at link 
> www.thenation.com/directory/ (from primary/primary)

The site is filtering offline browsers (including httrack). 
To avoid that, change the Browser identity (Set Option / 
Browser ID / Browser "identity" : set it to IE or 
Netscape) - but *first* ensure that you have setup 
reasonnable download settings, such as:
Set Options / Flow Control / Number of connections: 2
Set Options / Limits / Max transfer rate: 10000

Don't override robots and/or user-agent without setting up 
reasonnable bandwidth limits!