Please install the two items linked to from here: http://www.morearty.com/blog/2007/04/16/new-flash-player-and-also-a-flex-builder-patch/
There is a link to the debugger build of Flash (which you may already have, but maybe you got the release version), and also a patch for Flex Builder. The Flex Builder problem is the main one you're seeing. The issue is that with the latest release, the Flash player changed where they store the Netscape-plugin version of the player. They used to store it in <browserdir>\plugins, but now, they store it elsewhere (I think it's in <windows>\system32\macromed\flash), and they set a registry setting to point to it. The problem is that although the browser finds it in the right place, Flex Builder is looking for it in the old location, and thus displaying the warning message. Installing the patch will fix it. - Mike Morearty, Flex Builder team
