Parsing Flash embeded links is complicated
HTTrack uses Macromedia library to extract flash links
(so absolute/complex flash links won't be made relative) 

Even if the site has absolute or complex flash links, 
You can save all flash files if you: 
 1. Put all swf URLs in the Web Addresses for project
    (either manually or from Links/SiteMap page) 
 2. Option>>Scan Rules to only +*.swf or +*