> Within a website, I know that all files under a
> certain directory have an ".xls" extension and in
> another directory they are all ".pdf" but WinHTTrack
> is labelling them all as ".html" files.


What version of HTTrack are you using?  I quickly tested with 3.40 and things
look fine.  PDF was saved with .pdf and the XLS was saved with .xla (but still
loads normally in Excel).