1) Always post the ACTUAL command line used (or log file line two) so we know
what the site is, what ALL your settings are, etc.
2) Always post the URLs you're not getting and from what URL it is
referenced.
:
> httrack --update --priority=7 --display=2
> --search-index --can-go-up-and-down --retries=10
> --do-not-generate-errors --keep-alive
> <http://DOMAIN/index.php/Main_Page>
> -"DOMAIN/*/Special:*"
> +"DOMAIN/*/Special:SpecialPages"
> +"DOMAIN/*/Special:AllPages"
> +"DOMAIN/*/Special:ListRedirects"
> +"DOMAIN/*/Special:Statistics"
> +"DOMAIN/*/Special:Version"
> +"DOMAIN/*/Special:WhatLinksHere*" -"*?*"

So what URLs are you getting that are duplicates?