Yes, javascript problems are pretty common, due to the 
file's physical location and that URLs inside the JS are 
usually relative to the pages that call it.


Xavier mentioned a few threads back that he was planning to 
code some "smarts" into HTTrack to "understand" the 
relationship between a page and the JS file it calls.


Perhaps this made it into 3.30-a-05?  I've not tested yet.  
It does kind of sound like the usual javascript problems 
though.