Im a little late on this, but the Flex and Flex Builder teams just released updates to the Flex SDK and Flex Builder 3, which among other things, adds support for Adobe AIR 1.1.
There are also a ton of bug fixes for the Flex SDK and Flex Builder, as well as preliminary support for working with Flash Player 10 content in Flex Builder (although it is not clear where to download the debug player from. Im looking into this).
You can download the Flex 3.1 update from the Flex downloads page (it is build 220.127.116.1110 from Fri Aug 15 2008).
You can find information on how to update Flex Builder in this article (Im trying to find out if we have a downloadable installer).
Update (August 28, 2008) : The Flex Builder 3.0.1 update is now on the Flex Builder Updates page for download.