> Warning: Warning moved treated for 
> www.domain.tld/win/archive_01.zip (real one is 
> www.domain.tld/download/archive_01.zip)
> 
> The entire site is being downloaded EXCEPT the ZIPs.

Normally this warning means that httrack followed the link. 
Is there any file in the local directory 
<path>/www.domain.tld/win/archive_01.zip ?
Any errors in hts-log.txt ?