> Zip files aren't downloaded with this command:
> httrack <http://notepad-plus-plus.org/download/> -O
> "C:\Downloads" -T60 -R9 -r50 -n -N1003 %e50 -F
> Mozilla/5.0 -* +*zip
> 
> If the filters are removed from this commandline
> then the .zip files will be downloaded. How come? 

You said download nothing but zip. On that URL, there are NO ZIPs. That URL
auto forwards to <http://notepad-plus-plus.org/download/v6.3.3.html> but your
filter prevents that.

If you start on that page, you then run into
<http://download.tuxfamily.org/robots.txt> (the site where the zip is stored,)
and you didn't override robots.

There is only one zip file on the page, why don't you just use your browser,
right click, save as.