HTTrack follows standard links and downloads
  It won't follow drop down menus reliably
   (so offline menu can't work, reliably) 

  You could use Multi-Mirror or Link-List

  Try using "all sites in page (multiple Mirror)"  
   Put URL(s) in Project Web Addresses 
   <http://www.gateworld.net/sg1/index.shtml>
   <http://www.gateworld.net/atlantis/index.shtml>
   <http://www.gateworld.net/index.shtml>
   <http://www.gateworld.net/omnipedia/index.shtml>
   <http://www.gateworld.net/articles/index.shtml>
   <http://www.gateworld.net/articles/interviews/index.shtml>
   <http://www.gateworld.net/fanfic/index.shtml>
   <http://forum.gateworld.net/>
   <http://www.gateworld.net/store/index.shtml>

  OR 

  Try to: 
   1. Make .html link list of menu items
   2. Have HTTrack follow link list
    (HTTrack can follow Online & Offline pages)