> The above two links have the same formats except that 
they 
> are residing on different domain. Both links retrieve PDF 
> files. HTTrack did NOT capture the file from Link 1 but 
it 
> managed to capture file from Link 2.

It may have missed the first one because of mirror scope : 
use scan rules to widen the default scope, with something 
like +www.iwaw.net/04/proceedings.php*