> The site uses javascript to dynamically load a .js 
file depending on which browser you are using. I doubt 
HTTrack can interpret the code and know which files to 
grab.

Hum,

document.write('<Scr'+'ipt Language="JavaScript" 
Src="'+popbasedir+'popup'+peXt+'.js"></Scr'+'ipt>')

Yes, HTTrack will have troubles with this kindof code 
(expressions are HARD to parse!)