Hi,
I guess the Fullscreen feature was introduced mostly for video so that's why it defaults to that.
You need to do a bit of setup first to make sure you get the content you want in fullscreen.
I'd advise you to first set the desired scale mode and align for the stage.
e.g.
stage.align = StageAlign.TOP_LEFT;
stage.scaleMode = StageScaleMode.NO_SCALE;
then the important bit you need, the fullScreenSourceRect property:
//assuming you want to display 800 x 600 of you swf in fullscreen Mode
stage.fullScreenSourceRect = new Rectangle(0,0,800,600);
Goodluck!