finding same post twice.

After a long wait, the last updates of Post Indexer and Global Site search a couple of days ago both seem to be functioning well together. However- I fear my site setup may be causing some "duplicate content" issues. I now have 22 individual sites running under my main site. They are all set up as sub-domains and therefore http://www.subdomain1.com/post1 and http://www.subdomain1/mainsite.com/post1 return the same post. This causes Global Site Indexer to display the same post twice, 1 below the other and links 1 to 1 URL and 1 to the other. It seems to be duplicating every post in the network in search results. Does anyone have a solution for making it only index the the content on the individual sites? It seems like Google would take a dim view of the way this is working now. Not to mention the results take up twice the real estate on a page that it should.