> www.site.com/getpage.php?pagenumber=1
> www.site.com/getpage.php?pagenumber=2
> etc...
> 
> But HTTrack only downloads the first link, and
> change the rest of the links to the same page,
> ignoring the "?pagenumber=" part.

Httrack does this just fine. On disk you'll get files in the form of
getpageABCD.html

Post the log file with the real site url and options used and then someone
might be able to help.