I too had a similar experience. It can easily be corrected my manually configuring the popups xml file. While there are some minor bugs with the Application Builder, it does help do some things that were hard to do in the past. One thing in particular is the bookmarks. The Extent Helper only works if you are using the Web Mercator which I do not but the app builder allows me to create the bookmarks in my own coordinate system. Thanks Flex team for this new addition it was a much needed addition.
Josh White, AICP
Principal Planner
City of Arkansas City