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The only thing we have hit so far on Flex Viewer 2.5 running against ArcGIS Server 10.1 is related to security. When we secured a web service, the Flex Viewer 2.5 application presented the black box about the web service layer not being available. My Flex Viewer 3.0 presented the sign on box for the secured layer. Just an FYI that you will need to upgrade to at least Flex Viewer 3.0, if you want to start securing your web services.
Here is the link to a free ESRI one hour presentation on setting up your security on your web services, users, and roles.
Security Basics in 10.1: http://training.esri.com/gateway/index.cfm?fa=catalog.webCourseDetail&courseID=2596
Hope this helps!
Janie