This sounds like the known limitation in Silverlight with regards to the popups. In Silverlight the popups are generally not available in the main visual tree and WebUI Test Studio cannot access/automate those. Unfortunately Silverlight 4 does not include any improvements in this regard and we are looking to implement a work-around for the next product version.
I'm bookmarking this thread to follow up once we have a work-around for the popups automation limitation. In the meantime feel free to post any feedback you have both here in the forums or via support ticket if you prefer.
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