> I also have the same problem. PDF's are being saved as 
> HTML files. I had HTTrack create the debug log. Here is 
an 
> entry for one of the dynamic links to a PDF:
> [60] request for www.hvsinternational.com/Tracker/?>
fid=909&fxid=5&fx=pdf&fcid=345&rt=2:
> <<< GET /Tracker/?fid=909&fxid=5&fx=pdf&fcid=345&rt=2 

Option to change:
Spider / Check document type: if unknown

This should do the trick. If not, select "use old HTTP/1.0 
requests"