On the download page for the AIR SDK: http://www.adobe.com/devnet/air/air-sdk-download.html
It says: Note: Flex users will need to download the original AIR SDK without the new compiler. and provides separate links to SDKs that are about 15% smaller. Does anyone know the reasoning behind this? Are there compatibility reasons not to use the main AIR SDK that has a compiler? I'm still compiling my SWF with the compiler from the Flex SDK.

