I've been updating my copy of HTTrack when I see new 
versions have come out (great program btw =), but I've 
still noticed (although Javascript support has improved 
markedly in recent releases) that hyperlinks in DHTML menus 
(eg. like those created in Macromedia 
Dreamweaver/Fireworks) don't get recognised.

Maybe this is something you could look at in the next 
HTTrack release?