two things you need to do to get your swf working in AIR.
1. In Flash CS3 you need to add another layer as a solid object below all other objects. That will be your background.
If you don't, the swf will be transparent. This way you can choose if you want a BG or transparency.
2. Our system runs at 24FPS. Flash runs in 12FSP ( frames per second), so you need to fix it in your Flash CS3, and possibly re-arrange some of your animation.
Always glad to help,
Sean - MediaSignage.com