Flash files don't always work when published in Air. How do I fix this?

I have a program created in Flash CS5.5  When I publish it to Adobe Air, several things no longer work.  It is programmed so in some of the exercises, the user can use either the mouse or the space bar, but in Air, the space bar doesn't work.  It works fine in a Flash Projector.  Also, one of the files cannot be called up, and the User Name cannot be input.  All of these things work great in a Flash projector.  How do I get them to work in Air?