When I took over this website for a friend, in webmaster tools the previous dev did not set a preferred domain. The only property in webmaster tools was www version. He did have a 301 point to non www. I set up the non www property so that I could set the preferred domain to non www since the 301 was set up this way. Here's the thing that I'm confused about. He submitted the www sitemap to be indexed. The sitemap shows 100 pages indexed but the Index Status shows 5 pages. Does it matter that the indexed pages are www instead of being under the non www property? Or am I worrying about nothing?
I would stick to what was originally set up. As long as you have it set to non www as the prefered domain, the sitemap listing shows non www links and you maintain the same 301 direct, eventually it will get indexed (assuming there are no issues with the other 95 pages such as spamming / bad content etc).
Plan and simple, I would index the URL that you are selected as your "preferred" domain in your Google Webmasters account. I hope this has helped.
Just redirect the one to the other version and forget about this (use .htaccess file for doing this!)