To perform a successful initial content deployment from a publishing site the destination has to be an empty site.
This is not to be confused with the <blank> site template.
I have had some success when picking the <choose template later> option in the site creation page in Central Admin but sometimes even this fails.
The only sure way of creating a blank site is to use the following stsadm command
STSADM.EXE -o createsite -url <site-collection-url> -ownerlogin <domain\username> -owneremail <email@address>