These types of problems are more common than less common in Webmaster Tools sadly, GWT is often out dated or incorrect. GWT does not update as frequently as real time results and you often see these types of problems.
The Google Webmaster Tools Sitemaps Panel looks to be reporting correct as the picture shows that your only viewing that month and I imagine if you back track it it will come up with the rest, in regards of the top image with only 2 urls being indexed I believe this is the
non-www problem as you've mentioned since doing site:www.yourdomain.com reveals just one result but you need to include 1 more to that which is the domain so this equals 2, which is safe to say that the top image is displaying the www. data and not the non-www data.
Additionally if you haven't already you should add both www and non-www to Google Webmasters Tools, so your site is listed twice. One with www and another without www. and then you tell Google the preferred domain. While this isn't required for search results it may have to do with the results your getting within GWT.