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 
HTTP/1.0
<<< Referer: <http://www.hvsinternational.com/Services/?sid=12&v=ar>
<<< Cookie: $Version=1; 
ASP.NET_SessionId=pavfombl4de0kubdwinnnyrr; $Path=/
<<< Connection: close
<<< Host: www.hvsinternational.com
<<< User-Agent: Mozilla/4.5 (compatible; HTTrack 3.0x; 
Windows 98)
<<< Accept: image/gif, image/x-xbitmap, image/jpeg, 
image/pjpeg, image/svg+xml, */*
<<< Accept-Language: en, *
<<< Accept-Charset: iso-8859-1, iso-8859-*, utf-8
[60] response for
www.hvsinternational.com/Tracker/?fid=909&fxid=5&fx=pdf&fcid=345&rt=2:
code=200
>>> HTTP/1.1 200 OK
>>> Connection: close
>>> Date: Tue, 26 Aug 2003 14:37:03 GMT
>>> Server: Microsoft-IIS/6.0
>>> X-Powered-By: ASP.NET
>>> X-AspNet-Version: 1.1.4322
>>> content-disposition: attachment; filename=Feasibility 
Study of Expansion of Headquarters Hotel Capacity.PDF
>>> Cache-Control: private
>>> Content-Type: Application/pdf
>>> Content-Length: 1475264

We are really trying to get this work, but have had no 
sucess.