Originally Posted by tinafaye

Yes it would be a duplicate content issue if the same thing showed up on a subdomain and on a mapped virtual domain.

Solution: Setup the sub domains on a domain that is not pointing to your server, but is added to your server. Then google won't be able to find it, only the mapped domain name. (This is what I did in the past and it worked, no duplicate problems) -- There are also probably work arounds that can be done on the server directly, but since I am not a tech, I really can't comment there.