There is a bit of an issue in AIR with transparent windows and trying to drag them off the top of the screen when using nativeWindow.startMove(). In Windows XP and Vista you can drag them so that the nativeWindow.y is -17, less than which it will reposition them to -17 when you stop dragging. On Mac OS X and certain Linux setups, it won’t even let you drag the window off the top.
This isn’t much of a problem if your window is transparent merely to accommodate a custom chrome, but is if you have any substantial transparent area above your content any of the time (e.g. A window with controls/tooltips popping out above it, or room for a window to perform animation).