Blackbaud Case 12237846: I recreated your issue on our test servers and looked a little deeper into the issue. Something is buried deep in the code that is causing this duplication and it is not something we can address at this time. Because Query isn't intended to be a reporting tool, the typical recommendation is to create an Export to remove duplicates, but because you've created this query specifically to use on Dashboard, the best workaround I can give in this scenario is to simply ignore those duplicates.
In the near future (November I believe) the next version of Raiser's Edge will be released. On this, I know there are several new Dashboard enhancements.